NEWS.md
"Date", "POSIXct", or "POSIXt". Previous these columns either caused an error, or were not sorted. Now these columns are handled as numeric columns, and are converted using as.numeric(). Further, the actual error arose from converting a list to data.frame which failed for class "octmode". This step is avoided, since mmixedOrder() operates the same with list input anyway. An example is added to mixedSortDF() using output from file.info().heatmap_row_order(), heatmap_column_order()
which_heatmap which allows for returning the row or column order of a specific heatmap, when HeatmapList is provided. It works with horizontal side-by-side heatmap orientation, and vertical top-over-bottom heatmap orientation.class(x) to be any(X %in% class(x)).class(red) to reverse the order to "RGB" %in% class(red) in case red has multiple classes.keepOrder=TRUE, which checks for presence of "character" columns.writeOpenxlsx(), applyXlsxCategoricalColor()
data.frame, when called via writeOpenxlsx(). It was caused by using the option colRange to apply the categorical colors to a subset of data, providing substantial speed but at the expense of columns becoming out of sync for columns which were not continuously categorically colored starting at column 1. The bug is fixed."<br/>" with htmlOut=TRUE
comment=!htmlOut so htmlOut=TRUE by default turns off the comment prefix. Usually HTML output is for RMarkdown, where the comment prefix causes the text to become a heading, where the RMarkdown chunk option uses results='asis'.printDebug() intended for HTML output, using options htmlOut=TRUE and comment=FALSE specifically for RMarkdown output using chunk option results='asis'.More functions were updated for CRAN compliance, removing :::, including @examples and @returns.
options() for potential overridesx which was ignored anywayThe main update enables colorSub input as list for several functions: writeOpenxlsx(), kable_coloring(), and applyXlsxCategoricalFormat(). This feature enables passing a color function, or color assignments that are specific to each column in the data. The companion function platjam::design2colors() takes a data.frame and returns a list of colors or color functions, one per column, suitable for use directly in the functions updated above. The design2colors() function will likely move into colorjam.
colorSub now accepts a color list named by colnames, with either named character vector of colors for each column, or a function that takes column values and returns character colors for each value.names(colorSub) to cell values is slightly updated, mainly affecting color assignments for character strings that contain whitespace and punctuation characters.colorSub now accepts either character input as previously required, or now accepts list input named by colnames(x) whose list elements are either character vector of colors, or color function.applyXlsxCategoricalFormat() is called with one extra row to include the colnames, but it should be equivalent to previous behavior otherwise."A" can be colored red in one column, while "A" can be colored blue in another column. It also means that numeric columns can each have their own custom color function, which means it can exactly match a heatmap color function for example, instead of relying upon the limited conditional formatting available in MS Excel.moved to its own R file for convenience
removed dependency on dplyr
changed require() to check_pkg_available() to avoid attaching the kableExtra package.
argument colorSub now accepts three types of input:
character vector of colors named by column valuesfunction that takes column values and returns colorslist named by colnames(df), defining columns in each column using character or function as described above.colorSub as list input enables colorizing numeric columns by passing a color function: circlize::colorRamp2(colors=x, breaks=y)
new argument align to apply alignment per column, and retains proper alignment for numeric columns which are colorized (something kableExtra does not do by default).
new argument format.args for numeric column formatting by default, and is maintained even when numeric columns are colorized (which is also not handled by kableExtra by default).
new argument border_left,border_right which by default show a light grey left border per column
new argument extra_css which by default turns off word-wrap per column
new argument row.names passed to kableExtra::kable() but repeated to help determine the number of columns used for the left border.
keepNA=FALSE which allows NA conversion to "#FFFFFF" by grDevices::col2rgb(); with new option keepNA=TRUE which returns NA.options().data.frame with relevant coordinates.do_plot=TRUE to allow for suppressing the plot output and handling only the numeric values directly.minorLogTicks() resolved warnings.minorLogTicksAxis() resolved warnings.shadowText() resolved warnings.showColors() resolved warnings in the examples.rbindList() removed base R example that produced a warning.plotSmoothScatter() removed warnings.dex as replacement for gradientWtFactor, reflecting the same argument in color2gradient(). This argument is only used when a single color is provided, in order to create a color gradient using that color. The argument dex improves the color tone, which more closely matches the original color without becoming too de-saturated during the process.gradientWtFactor=NULL so this argument is ignored, in favor of new argument dex=1.dex now accepts values at or below zero, by converting them to fractions.grepls() now properly works with regular expressions when searching a list of package functions. Also added unit tests to confirm this use case.cPaste() and mixedSort() functions.getColorRamp() fixed rare edge case with a named palette, using n=NULL (so it returns a color function), and the palette was reversed.multienrichjam::gsubs() into jamba. During the process, it was noted that input x could not be a list, which is inconsistent with other functions such as lengths(). It now processes list input either iteratively (if input is a nested list), or as unlisted subsets for optimal performance.asp with optional ability to define a fixed aspect ratio. When enabled, the plot xlim and ylim behaves slightly differently, but consistent with plot(), plot.default(), and plot.window(), which include at least xlim and ylim but expand one axis if needed in order to obtain the fixed aspect ratio.add=TRUE the xlim and ylim values by default will use the plot device range, instead of the data value range. This change makes the density consistently calculated for the plot area used for display.fillBackground=TRUE changed from using usrPar() to using grid::grid.rect(). However, grid::grid.rect() apparently honors the plot device itself only when par("xpd"=FALSE) and after abline() is called with non-empty and non-infinite value for h or v. Weird. Nonetheless, it causes grid::grid.rect() to crop output to the plot device, which has the benefit of resizing to the plot device when asp aspect ratio is defined, when the device is resized. Normally usrBox() draws a box with fixed coordinates, and with asp is defined the xlim and ylim will change with the plot device is resized. In future, if the grid::grid.rect() method is problematic, the method will need to revert back to using usrPar().circlize::colorRamp2() color function, a recently updated version of circlize now stores colors internally as R hex colors, instead of previous versions which stored numeric matrix of r,g,b color values.circlize::colorRamp2() data are numeric matrix of r,g,b values, or character vector of R colors. It should therefore be robust to earlier or newer versions of circlize:: colorRamp2() color functions.doPlot=TRUE which allows disabling the graphical output, mainly motivated by the desire to create unit tests.startRow, startCol to define starting row and column, repectively, for a new worksheet.doFilter=FALSE was being ignored, since the default worksheet created by openxlsx::writeDataTable() already enabled column filtering by default. This argument is applied properly now.startCol consistent with the same argument in writeOpenxlsx(), and cols used to specify an exact vector of columns. The arguments allow loading data starting at a specific column or for specific columns in each Excel worksheet.Added simple unit tests to verify that a data.frame saved by writeOpenxlsx() and re-loaded by readOpenxlsx(), optionally using startRow and startCol, will reproduce the identical input data.frame.
Fixed errors caused by if(class(x) %in% x) since class(x) can have >1 value, an error on R-4 and only a warning on R-3.
imageByColors() and handleArgsText() which called iteratively by the argument-printing utility jargs().cache.lazy=FALSE the cache files did not save .rdx and .rdb files, causing this function to fail. In that case the .RData files can be loaded but not using lazyLoad() so they are loaded directly into the environment envir. See changes below.new argument options: file_sort=c("globals", "objects") which defines the file order by default to use the order they appear in the RMarkdown index files "__globals" or "__objects". Both files should be present, and should be identical, but the option is there to choose one or the other.
Using globals is the new default, as it is more reliable than using file creation time:
new argument: preferred_load_types=c("lazyLoad", "load") to help limit the mechanism used to load cache objects. When .rdx/.rdb files exists, the default is to use lazyLoad(). When they do not exist, .RData files typically always exist, and can be loaded with load(). The option now exists to prevent lazyLoad() and to use load() instead. Subtle difference in how R objects are stored and re-used.
numerous functions had argument help text updated for clarity.
mixedSorts(), cPasteS(), cPasteSU()
NULL, output now retains NULL without error.names(x) for input data.function input from circlize::colorRamp2()
character function name with optional package prefix.preset_type to position labels either at the plot frame (default), or preset_type="figure" will position labels relative to the margin around each figure.marginUnit to specify whether to display margin units in lines marginUnit="lines" (default) or inches marginUnit="inches".mixedSort() and mixedOrder() used similar but non-identical logic when applying ignore.case=TRUE and useCaseTiebreak=TRUE.
mixedOrder() (as it should have been), and the logic was corrected to fix weird edge cases of internal capitalization within a mixed character/numeric string.sort(), though I admit it feels weird. Default sort() returns c("aardvark", "Aardvark", "abacus", "Abacus").mixedSort() by almost two-fold for default settings, avoiding almost duplicating the same sort logic just to apply the case-sensitive tiebreaker. I mentioned that time hit in previous NEWS.Optimized to handle mixed-class, and nested or simple list.
When the input list contains multiple classes
list otherwise class conversions (which help optimization) cause problems with factor and character types. For some reason, when calling unlist(x) and x contains factor and character, the output is converted to character (which is fine), however factor values are converted to integer then character strings of the integer values.mixedSorts() on subsets of x with the same class, so each subset is run with single-class optimization. Now instead of scaling with length(x) it scales with length(class(x)), obviously much faster.When input list is nested, and content is all the same class, it runs mixedSorts() on all data en masse as is optimal.
When input list is nested, and content has different classes, each subset is sorted within its class, so list is sorted within its own subgroup. For inconsistently nested list structure, various branches will be sorted together, which is slightly unoptimal, but it does maintain the input class of each atomic vector.
All classes are maintained, without coersion to character.
honorFactor=keepFactors when calling mixedSorts(), which should provide a notable speed boost, in addition to optimizations to mixedSorts() already described.Began prep for eventual CRAN release.
ComplexHeatmap to Suggests.heatmap_row_order() and heatmap_column_order() to check for ComplexHeatmap.check_header=FALSE to sidestep issues with column headers that do not align with subsequent data.formatInt(), rmNA(), asSize(), sizeAsNum(), imageByColors()
class(x), to allow multiple values.mixedSort(), mixedOrder() default honorFactor=FALSE in vector context.
mixedSortDF(), mmixedOrder() default honorFactor=TRUE in data.frame or list context.
data.frame, they expect mixedSorted character columns, and sorted factor levels. For someone mmixedOrdering a list, they expect character vectors to be mixedSorted and factors to be sorted by level.mixedSort(), mixedOrder(). mmixedOrder(), mixedSortDF()
gasp These core functions were ignoring honorFactor=FALSE and were instead always keeping factor level order without imposing its own sort order.
The intent was to use honorFactor=FALSE, which was supposed to be consistent with previous versions of jamba. However, other dependent Jam functions became somewhat reliant on unintended behavior which represents honorFactor=TRUE. This behavior is most important for uses of mixedSortDF() which is expected to honor factor level order by default. This expectation enables other assumptions about the order of values. That said, specific errors have been rare or non-existent thus far.
A “problem” arises only in R versions before R-4.0.0, where default R-3.6.1 options(stringsAsFactors=TRUE) causes data.frame() to convert character to factor. During the conversion, factor level order is defined using vanilla sort(). Therefore, using mixedSortDF() appears to use vanilla sort order by honoring the factor level order, but only in cases where the data.frame was created by a method that did not override options(stringsAsFactors=TRUE) for consistency. So the use of honorFactor=TRUE by mixedSortDF() causes an edge case of inconsistent order for some data.frame objects, dependent upon the value of getOption("stringsAsFactors").
The resolution to above issues:
mixedSortDF() should continue to do what is expected, which in my opinion is to honor factor order by default; andstringsAsFactors=TRUE to wreack havoc should themselves be fixed. “Check yourself, before you wreck yourself.” I shouldn’t have said that.So the resolution overall is to have different defaults for honorFactor, even though it seems improper. I argue that it is proper:
mixedSort(..., honorFactor=FALSE) because someone calling mixedSort() is doing so for the benefit of mixedSort behavior, otherwise they can call sort() on a factor and get the same result as mixedSort(..., honorFactor=TRUE). Therefore I think honorFactor=FALSE is expected for a vector.mixedSortDF(..., honorFactor=TRUE) because someone calling mixedSortDF() is doing so for the benefit of sorting character columns using mixedSort() logic, otherwise their factor columns are assumed to have carefully (let’s hope) constructed factor levels. And since those factor levels are so dear to the analyst, their order will be maintained when sorting a multi-column data.frame. (Or equivalent tibble, DataFrame, etc.) Therefore I think honorFactor=TRUE is expected for a data.frame.mixedOrder(..., honorFactor=FALSE), due to vector context.mixedSorts(..., honorFactor=TRUE), due to list context.mmixedOrder(..., honorFactor=TRUE), due to list context.cPaste() was not properly enforcing na.rm=TRUE, which caused NA values to be converted into "NA". The bug also affected cPasteS(), cPasteU(), and cPasteSU(), along with dependent functions in the genejam package.
cPaste() now calls rmNAs() when na.rm=TRUE, to remove NA values in relatively efficient manner across the input list x.cPaste() new argument useLegacy will optionally enable the previous code, which was optimized for list that contain vectors with identical classes throughout. It had the limitation that it did not preserve factor level order, and sometimes converted factor to character in mixed list.rgb2col() by checking if input argument red was empty length(red)==0, or NA is.na(red). However, when red has length(red)>1 the second check for NA results in a logical vector of TRUE/FALSE, only the first of which is used in the if statement. New versions of R invoke a warning, but future versions will eventually cause an error. Nonetheless the code was updated to check for all entries in red like this: all(is.na(red)).printDebug() several arguments use getOption():
jam.htmlOut, jam.comment are logical and intended for usage inside Rmarkdown documents, to customize the output.jam.file, jam.append, jam.invert, jam.formatNumbers, jam.trim, jam.big.mark, jam.small.mark
htmlOut=TRUE now properly includes "<br/>" to force a line break after the output.mixedSorts() uses iterative mixedSort() when there are different classes contained in x, otherwise factor values are converted to integer strings.
mixedSort() was re-defining factor levels using the order of unique values, instead of the original levels. It was changed to use levels.
mixedSort(), mixedOrder(), mixedSorts() new argument.
honorFactor=FALSE keeps previous legacy behavior, which is to perform alphanumeric sort on character values even in factor columns. However, now this behavior can be changed.rowGroupMeans() argument rmOutliers=TRUE along with crossGroupMad=TRUE incorrectly caused the rowStatsFunc to be redefined. This bug was fixed. Also, when returnType="output" it no longer returns the attributes "n" and "nLabel" which are intended to represent the number of non-NA replicates per group, and this information is not relevant to the input data.printDebug() bug fixed:
bgText had length=1, or any element in the list had length=1.color_dither() simply takes one color, and returns two colors that differ by a minimum contrast, with the same hue. Not coincidentally it substitutes into the printDebug() function.cell_fun_label() was updated to skip cells with no text, vastly improving rendering speed for heatmaps that contain a large proportion of blank labels.printDebug() was updated:
indent is honored, previously ignored. When numeric it defines the number of character spaces " " used to indent.color2gradient() is called using dex=1 instead of gradientWtFactor=1, which should apply more consistent scaling to light and dark colors.dex used to control intensity of light,dark color adjustment. When dex=0 no adjustment is performed.bgText light,dark adjustment now uses dex as well, for consistency.doColor=FALSE, the output enforces conversion of factor to character when combining multiple values into a string, consistent with doColor > 0 behavior. Should be minor effect if any.setPrompt() updates:
debug to print the control charactersaddEscapes=NULL, where it autodetects whether it is running inside RStudio, setting addEscapes=TRUE if not running inside RStudio. When addEscapes is defined, that setting is honored.default box color is much lighter, less saturated.
new argument panelWidth to size labels to plot panel width, mostly useful for labels at the top or bottom of each plot panel. This argument is intended to be used by the jamma package to place plot panels above each plot, at least the full width of each plot panel.
panelWidth="force" labels always equal full panel widthpanelWidth="minimum" labels are at least full name width, or as wide as necessary for the text labelpanelWidth="maximum" labels are as large as needed for text label but no wider than the plot panel.col2hsl() and hsl2col() help convert colors to and from HSL color space
col2hsl() for visual comparison between HCL and HSLfarver package, and may become a formal dependency of jamba.S=100 and L=50. With HCL, every hue has its own local Luminance values for the maximum Chroma, and the maximum Chroma varies substantially across all hues.breaksByVector() was updated to:
breakPoints and labelPoints to represent the unique values in the order they appear.breakLengths to the output list for convenience.imageByColors() adjustments
imageByColors into its own R file jamba-imagebycolors.R.doTest=TRUE, which now returns test data invisibly.cexCellnote input is somewhat confusing and may change in future. To supply cex values for each column or row, use list input for cexCellnote, where each list element represents a column or row, respectively.showColors() was updated to accept color functions in two forms:
circlize::colorRamp2() form, which contains attributes "colors" and "breaks" that define the underlying color gradient. These colors are converted to hex, named by "breaks", then displayed.function are expected to accept an integer number, and return that many colors, which are named by the integer index, with default length n=7.showColors() updates:
par("mar") properly, and to return NULL when input is empty, instead of throwing an error.makeUnique=TRUE to display the first unique color in each color vector.pasteByRowsOrdered()
keepOrder=FALSE, no change to default behavior. When keepOrder=TRUE, any character columns are converted to factor whose levels are defined by the order of unique existing entries, keeping the order provided in x.byCols passed to mixedSortDF() to define the order of column sort for factor levels. This argument was previously passed via ..., but was added as a specific argument to make this connection more apparent.call_fn_ellipsis() was added.
... to a function that does not permit ... but which may match some argument names in ....call_fn_ellipsis() only passes named arguments that are permitted in the subsequent function.some_function_call(x, ...)
call_fn_ellipsis(some_function_call, x, ...)
rowGroupRmOutliers() is a convenience function that calls rowGroupMeans(..., rmOutliers=TRUE, returnType="input").
crossGroupMad=TRUE calcualted the row MAD value using the median MAD per row, using non-NA and non-zero MAD values. See description of changes below.Moved rowGroupMeans() and rowRmMadOutliers() into a specific .R file for easier management.
rowGroupMeans() changes when rmOutliers=TRUE:
new argument crossGroupMad=TRUE will:
rowMadValues
rowMadValues is defined as minDiff
rowMadValues and minDiff are passed to rowRmMadOutliers() for each group, which therefore applies the same threshold to each group on a row, and with the same minDiff difference-from-median required.0 unless all groups have MAD=0 on the same row.minDiff will by default require a point to differ at least more than the median difference observed from median in each row, in each group. If all MAD=0 in all groups and all rows, then minDiff=0 in which case it likely does not have adverse effect.rowRmMadOutliers() changes:
rowMadValues can define the MAD values on each row, useful for setting the per-row MAD across multiple sample groups for example.minReps to require this many non-NA values, only useful when providing rowMadValues values, and for rows that have n=2 replicates.includeAttributes=TRUE now includes attribute "outlierDF" which is a a data.frame with summary information for each row in input x.writeOpenxlsx() changes
wb to supply an existing Workbook object, instead of loading it from a file.Workbook object with invisible(wb).file=NULL then output is not saved.Workbook object, then save that Workbook one time at the end.colWidths will apply column widths to the Workbook internally, to avoid having to save, read, apply, and save.applyXlsxConditionalFormat(), applyXlsxCategoricalFormat(), set_xlsx_colwidths(), set_xlsx_rowheights()
xlsxFile can be a filename or Workbook objectWorkbook invisiblymixedSortDF() was updated:
df input objects with zero rows are returned directly.NA for empty rownames, but caused an error when the df had zero rows, since NA has length 1 and did not match the number of rows. First, zero-row objects are returned, no need to sort. Second, the section was rewritten to be more robust, now empty rownames are removed prior to calling mmixedOrder().byCols for data with no colnames, useful when sorting by "rownames".plotRidges() is analogous to plotPolygonDensity() except that it uses ggplot2 and ggridges to plot density profiles inside the same panel. Particularly good for comparing densities across columns/samples, and when there are a large number of samples.
cell_fun_label() is a wrapper function to add text labels to ComplexHeatmap::Heatmap(). It is somewhat configurable:
setTextContrastColor().1502110 would be displayed 1.5M.reload_rmarkdown_cache() will load the cache files stored after processing an Rmarkdown .Rmd file. It is intended to help restore the Rmarkdown data available to particular Rmarkdown chunks, or to restore the entire session so the data can be used for more analysis or visualization.
environment
color2gradient() new argument default gradientWtFactor=NULL:
gradientWtFactor controls the intensity of the light-to-dark color gradient, where gradientWtFactor >= 1 defines a broader range from light-to-dark, and gradientWtFactor < 1 defines a more limited light-to-dark. For example, when n=2 it there does not need to be as large a difference in brightness for color1 and color2.gradientWtFactor based upon n.color2gradient() argument gradientWtFactor can be supplied as a vector, so the value will be applied to each gradient created, in order.
mixedSortDF() had a bug when supplied with matrix that had no rownames(), it would fail because the intermediate data.frame was assigned rownamesX=rownames(x) and thus had zero length. It now assigns rownamesX=rmNULL(nullValue=NA, rownames(x)) which fills the column with NA values.Ported two functions from multienrichjam.
heatmap_row_order(), heatmap_column_order() are specifically used with Bioconductor package ComplexHeatmap heatmaps. These functions were enhanced to handle several scenarios: presence of absence of row_groups, column_groups; with and without rownames(), colnames() in the data matrix; with and without specific row_labels, column_labels.diff_functions() is a simple utility function intended to compare the text in two functions, motivated while migrating functions into R packages, while needing to make changes in the old function source, propagating to the new function source. Currently the function requires access to commandline tool "diff" which likely limits this function to linux-like operating systems, MS Windows System Linux (WSL), or Cygwin on MS Windows.plotSmoothScatter() was improperly defining xlab and ylab when supplied with a data.frame or matrix with colnames. The steps now closely match graphics::plot.default().noiseFloor() was not checking for minimum to be NULL, though this error has not occurred myself, that step is now performed as it would have thrown an error.renameColumn() when the to values were supplied as factor values, they were coerced by R into integer and therefore lost the character string values provided. The workaround is to coerce to with as.character() which is straightforward for processes outside renameColumn(), however the expected behavior is certainly to maintain the character string, so this function has been updated accordingly. The situation tends to happen when the column renaming is stored inside a data.frame and the rename “to” column type factor is not checked beforehand. It is a rare scenario, but warrants a fix. In addition, renameColumn() also operates on GRanges and related genomic ranges objects, and that step requires IRanges::values() generic function. The values() functions were updated to include the proper package prefix, in the event those packages had not already been loaded. This function now explicitly requires length(from) == length(to). The help text was updated with more information.mixedSortDF() argument default useRownames=TRUE was changed to useRownames=FALSE to protect against extremely slow sort behavior with large nrow data, which would previously by default sort all rownames even when not required. The new behavior only sorts the columns specified, and can enable rownames as a tie-breaker with useRownames=TRUE or by including byCols=0.getColorRamp() now accepts gradient names supplied by colorjam::jam_linear and colorjam::jam_divergent, when the "colorjam" R package is available. The linear gradients differ mainly in subtle ways, emphasizing more color saturation in the mid-range values, motivated by their use in coverage heatmaps.mmixedOrder() was apparently enabling verbose output by default by using verbose - 1, and how did I not realize that if (-1) cat ("yes") would print "yes"? Geez. This bug also caused mixedSort() and mixedSortDF() to print extremely verbose output by default.Reminder to myself to use options(pkgdown.internet=FALSE) when behind VPN. And sometimes when not behind VPN…
sizeToNum() performs the opposite function as asSize(), it takes an abbreviated size as a character string, and converts to numeric value.mmixedOrder() was updated to fix a bug when sorting numbers with class "integer64", which is defined by bit64::integer64. These values were produced by openxlsx::read.xlsx() that contained large integer values, and were previously ignored by mmixedOrder(). The change also fixes a bug in mixedSortDF(), however this bug did not affect mixedSort() and mixedOrder(). The conditional now tests is.numeric() which returns TRUE for bit64::integer64 types, and hopefully this logic will work for future large numeric types.mixedSort() fixed an issue where ignore.case=TRUE caused factors to be sorted alphanumerically instead of by factor level. The new and intended behavior is to sort by the unique uppercase factor levels, otherwise maintaining the factor level order.rbindList() was updated to change the way returnDF=TRUE is handled. It now simply calls data.frame(x, check.names=FALSE), with no further validation. Previously this option called a function unlistDataFrame() that did not get ported into jamba, and probably will not.mixedSortDF() was enhanced to allow row name sort, using these formats: byCols="rownames" or byCols="row.names" or byCols=c(0). Reverse row name sort can be accomplished by byCols="-rownames" or byCols="-row.names" or byCols=c(-0.01). When byCols contains numeric values, the sign is taken first so any negative values will reverse the sort, then values are rounded to integer values. So byCols=-0.1 will reverse sort by row names, useful when it is more convenient to provide byCols as a numeric vector than a character vector.
mixedSort() was refactored to simplify the logic, and to correct small issues, for example when ignore.case=TRUE and x is a factor, the previous behavior would call toupper() which converts x to character, and which is sorted as such. The new intended behavior is to sort by unique(toupper(levels(x))) to maintain factor level order as defined. The new logic defines a transform function for x, whose output is passed to mixedOrder(). For example, when sortByName=TRUE the transform function passes names(x) to mixedOrder(). Otherwise, there is only one call to mixedOrder() and no data is copied during the process, which should be reasonably memory-efficient for large sort operations. Frankly, it needs one more refactor to push all the logic into mixedSort().
mixedSortDF(), mixedSort(), and mmixedOrder() had arguments extended to represent all arguments in mixedOrder(), so the sort customizations are properly passed between functions.
Some R functions were moved into separate files for easier management. More work should be done over time to reduce the number of functions in each file. Some files have 15 to 31 functions!
asSize() was moved from jamba.R into jamba-size.R.mixedSort() functions were moved into jamba-mixedSort.R.lldf() new argument use_utils_objectsize=TRUE to prefer utils::object.size() instead of pryr::object_size() after observing some cases where object sizes were vastly over-stated for unusual Bioconductor object types. It is unclear to me exactly how the memory usage is determined, and which function is correct, so for now the two alternatives will remain in lldf().readOpenxlsx() was updated to fix a small bug when loading multiple sheets in one pass. It should now work as expected to run readOpenxlsx() on any xlsx file, and return a list of data.frame objects representing each worksheet in the xlsx file.
readOpenxlsx() new arguments check_header and check_header_n are intended to check for header rows, recognized as rows with a different number of columns than subsequent rows of data in each sheet. When check_header=TRUE it will check the first check_header_n rows to determine ncol() and sclass() on each row loaded individually. When header rows are detected, the first value of the first row is assigned to column dimnames of the data.frame returned, and the full header data is included as an attribute attr(df, "header"). This method is intended to help when loading multiple worksheets, and none, some, or all worksheets may have header rows.
Note this methodology is being tested currently, to debug edge cases where data is sometimes detected to have fewer columns in some rows than others. The intent is to expect skipEmptyCols=FALSE to return all columns even when there is no data present, for consistent ncol() from data rows, and fewer columns for header rows. The logic may be updated over time.
readOpenxlsx() was updated to apply skipEmptyCols=FALSE by default for each step, to avoid inconsistencies especially when the column headers are not defined for all columns, or data is not present in all columns with column headers.
rowGroupMeans() was updated to remove a silent dependency on matrixStats and now properly checks the dependency, and calls with prefix matrixStats::rowMedians() and matrixStats::rowMads() as needed.applyXlsxCategoricalFormat() was updated to streamline the categorical color matching, though not by much for large files. Will revisit and improve speed eventually.igrepl() is a convenient wrapper for grepl(..., ignore-case=TRUE)
writeOpenxlsx() new argument wrapCells=FALSE changes the previous behavior so that cells are not word-wrapped by default. Previously, when column width did not accomodate the text, cells would be tall - and sometimes “super-tall”. The function set_xlsx_rowheights() can be used to fix this situation, however that process can be quite slow for large Excel worksheets.provigrep() argument maxValues had not beedn implemented properly when applying a limit to returned values per grep pattern. This implementation has been corrected. Examples have been updated to demonstrate its utility.heads() applies head() across a list of atomic vectors, using a one-step style that is notably faster than lapply(x, head, n) especially for long lists. Also it can apply a vector of n values if needed. Its main utility is for provigrep() with argument maxValues.proigrep() was added as a lightweight alias to provigrep(..., value=FALSE) which returns the index positions rather than the values.match_unique() matches unique vector values to the full vector. I found myself performing this step so many times I thought a function might feel better. It may also be equivalent to which(!duplicated(x)) - but again, that doesn’t feel easy enough. I guess.lldf() is a lightweight extension to utils::ls() that returns a data.frame with object name and size, sorted largest to smallest. I found myself using this function several times after becoming more aware of object sizes while using jamsession::save_jamsession().plotSmoothScatter() default argument bandwidthN=NULL which changes the default bandwidth to use bwpi for the per-inch calculation of the bandwidth that can be reasonably displayed given the output size. Previous default was bandwidthN=300. Note that the output density calculation is dependent upon the display size, which can affect the results.plotSmoothScatter() now honors xlab and ylab, and when those are not provided, it uses base R convention and applies deparse(substitute(x)) to determine a suitable default label.shadowText() new argument shadowOrder to control the rendering of shadows and labels for a vector of labels: shadowOrder="each" renders each shadow then each label in order, so that subsequent shadows will overlap previously rendered labels; shadowOrder="all" renders all shadows at once then all labels, so that shadows will never overlap labels. Very minor issue, mostly affecting display of labels that slightly overlap - see examples in shadowText().setCLranges() fixed issue in first time processing, which was wrongly defining Crange and Lrange for future use even inside Rstudio. (Minor issue that would only affect text labels with light colors on a light background.)fix_matrix_ratio() had a bug in secondary logic referring to non-existent object y. This function is used as an optional backend for imageDefault when useRaster=TRUE to provide reasonable default matrix adjustment to reduce or prevent visual distortion when image interpolation is performed on matrices with non-1:1 ratio of rows and columns.readOpenxlsx() is the reciprocal to writeOpenxlsx() that differs from openxlsx::read.xlsx() mainly in that it loads multiple sheets at a time, and does not mangle column names when check.names=FALSE. The openxlsx method behaves as if check.names=TRUE in all cases, as of 01-Dec-2020.getColorRamp() argument defaultBaseColor="grey99" from the previous defaultBaseColor="grey95" which just felt too dark.plotSmoothScatter() new argument col passed to smoothScatterJam() to be compatible with smoothScatter(), this defines point color when nrpoints is non-zero. Apparently not defining this argument allowed R to do fuzzy argument name matching, causing conflict with colramp.plotSmoothScatter() new argument expand will expand the x-axis and y-axis ranges by this amount. The default expand=c(0.04, 0.04) mimics the default setting for R base plots. The help text was updated.plotSmoothScatter() now uses grDevices::xy.coords() to define coordinates, avoiding internal logic that essentially did the same thing. This change should be silent. This change does remove the warnings that were produced with input supplied as a single numeric vector.plotSmoothScatter() argument binpi was setting the bins per inch identically for x and y axes, using the maximum size – when it can and now does handle each axis independently. Now the output pixels should be square, rather than being influenced by the ratio of the plot device.getColorRamp() was updated for single-color input and defaultBaseColor. It now properly creates a color gradient from light-to-dark, or dark-to-light based upon the relative brightness of color and defaultBaseColor.Updates to setCLranges() mainly affect colorized console text output, used by printDebug() which calls make_styles(). This function is also useful to adjust a color or vector of colors for contrast on a light or dark background.
setCLranges() argument has new default lightMode=NULL and slightly different, more intuitive behavior. When lightMode is defined (TRUE or FALSE) then it over-rides existing values, and uses the corresponding lightMode setting directly. Otherwise, when lightMode=NULL any existing Crange and Lrange values are used. If none are defined, then checkLightMode() is called, then default values are used.setCLranges() were updated so the argument default lightMode=NULL is used. When those functions are called with lightMode=TRUE or lightMode=FALSE the text output will be adjusted. For example:printDebug("yellow", lightMode=FALSE)
printDebug("yellow", lightMode=TRUE)Functions affected: * checkLightMode() * applyCLrange() * setCLranges() * printDebug() * make_styles() * jargs()
printDebug() failed on class "package_version" ultimately because unnestList() could not unlist this object type. The “package_version” class is a list, e.g. is.list(packageVersion("base")) is TRUE. However, accessing the first item, e.g. x[[1]] always returns the full object unchanged… which is not expected behavior for a list. This class was added to stopClasses.unnestList() was refactored to handle nested lists with and without names in various combinations, and to use tryCatch() as a final protection from infinite recursion, when list-list objects do not behave like list objects (as is the case with the "package_version" class.)applyCLranges() was updated to remove the warning message for argument fixYellow that read "the condition has length > 1 and only the first element will be used". The function now handles vector input for fixYellow and extends the vector to the length of x.plotSmoothScatter() now correctly determines the plot aspect ratio after the plot is initiated. The situation occurs when using graphics::layout() which does not update the par() settings until the plot is created. Now a blank plot is initiated before determining aspect ratio, which allows proper calculation of the 2D density plot.plotSmoothScatter() new argument binpi defines the nbin number of displayed bins based upon plot panel size. The default binpi=50 defines 50 display bins per inch. This value will adjust accordingly for large and small figures, based upon the physical size of the figure in inches.plotSmoothScatter() argument nbin new default is nbin=NULL, which then uses binpi to calculate nbin. To use the previous style, set nbin=256 which will ignore binpi.plotSmoothScatter() new argument bwpi defines bandwidthN based upon the plot panel size. The default bwpi=NULL does not implement this scaling by default, instead bandwidthN=300 is still the default. The benefit of using bwpi is mostly in speed of calculating 2D density for multi-panel plots where detail would already be lost during display.plotSmoothScatter() uses two arguments to determine how data is plotted:
bandwidthN defines the number of bandwidth divisions on the x- and y-axes used to calculate the 2D density. Higher bandwidthN calculates greater detail in the 2D density – these values are all typically higher than graphics::smoothScatter(), and this is still the driving reason to use plotSmoothScatter and not smoothScatter().nbin defines the number of visible pixels used to display the calculated 2D density. Higher nbin creates visually more detailed representation of the 2D density.Usually nbin and bandwidthN values are similar to each other, since it conceptually makes sense to calculate 2D density at roughly the resolution used to display the results. These arguments are adjustable and are still valid for most purposes.
So why the change? The short summary is that multi-panel plots have fewer pixels being displayed, and I wanted a convenient method to reduce the number of pixels (nbin) displayed in each panel. (Truth be told, while working from home creating plots on remote servers, I noticed just how long multi-panel plots take to render. Most of that time is spent rendering detail never seen during display.)
After some extended testing, I concluded that bandwidth should remain relatively constant regardless of the display pixels, in order to maintain consistent 2D density despite the image size. (Conceptually, it makes sense that the image display size should not affect underlying calculation of the data to be displayed.) However, the number of displayed pixels should be reduced roughly proportional to the size of the plot panel, which solves the issue I was having of plotting data with far more detail than could be visually rendered, making plots larger, take longer to display, and creating larger saved file sizes.
Also, the resolution of the resulting plot can now be adjusted relative to the output plot size, consistent with computer monitor resolution (dots per inch dpi), and printed paper output dpi.
applyXlsxConditionalFormat() and writeOpenxlsx() were updated to make default colors in numStyle, intStyle, pvalueStyle slightly more colorful, while also being less dark, so Excel default black text has better visible contrast. (Why can Excel not apply conditional format rules to text font color?)writeOpenxlsx() format for P-values pvalueFormat formats values above 0.01 as decimal value such as 0.022 or 0.157, P-values below 0.01 are exponential notation such as 2.31E-10. (I wish R could avoid formatting things like 1.1e+00 and 1.0e+01 without using a custom function.)writeOpenxlsx() was updated with a more comprehensive example.applyCategoricalFormat() has a simple working example.applyXlsxConditionalFormat() has a simple working example.set_xlsx_rowheights() and set_xlsx_colwidths() are light wrappers to the very useful functions openxlsx::setRowHeights() and openxlsx::setColWidths(). They simply open the workbook, apply the values to the appropriate sheet, then save the workbook.setPrompt() by default wraps the color sequence inside proper ansi escape sequences, which helps the console properly apply word wrapping by ignoring color sequences in the estimate of character count per line.printDebug() fixed a visual glitch caused by using gsub() to remove trailing sep characters from vector elements before adding the sep itself, without removing ANSI-encoding from the sep string, sometimes removing trailing zero from numeric strings but only in the middle of a multi-element vector. Now the sep is appended only using paste0() and no trailing sep characters are checked nor removed. This behavior is probably better since it should properly represent the input content.printDebug() was modified to fix a longstanding visual glitch that would not fully reset inverted ANSI colors that span multiple lines. If the output uses color, a trailing crayon::reset("") is added to the end of each line.jam_rapply() is a lightweight customization to base::rapply(), specifically designed to keep NULL entries without dropping them silently. It has the added benefit of being able to flatten a nested input list, then expand back into the original nested list structure, without losing the NULL entries.A theme of several updates this version has been to handle list input that may contain factor and non-factor vectors. In fact even handling a list of factor vectors is unclear at least to me. For example, base::unlist() operating on a list of factors will define one factor vector whose levels are literally the unique first-occurrence of each factor level. For example sort(factor(c("A","B"), levels=c("A","B"))) results in c("A", "B"), while sort(factor(c("A","B"), levels=c("B","A"))) results in c("B", "A"). So what should be done when given:
list(factor(c("A","B"), levels=c("A","B")), factor(c("A","B"), levels=c("B","A"))
In reality, most such occurrences would not happen, if factor levels are specified, the best solution is to include the full set of factor levels with each factor vector. But if the input contains a mixture of factor and character, vectors, running unlist() converts factors to integers… which is really bad. At the very least I had to handle and prevent that scenario.
pasteByRowOrdered() was modified in two ways: new argument na.last=TRUE is passed to mixedSortDF() to allow NA values to be sorted at the top, which seems intuitive for most scenarios; also the ... additional arguments are passed to mixedSortDF() which allows column sort order to be customized. Previously pasteByRowOrdered() called mixedSortDF() which sorted columns in the order they appear in the data.frame, however sometimes it is better to sort columns differently, while keeping the original column order intact. See examples for illustration of na.last=TRUE. In a two-column table with NA values in the second column, using na.last=TRUE (default) would yield factor levels c("A_B", "A", "B_C", "B"), while using na.last=FALSE would yield c("A", "A_B", "B", "B_C"). This output seems more intuitive, however the default in mixedSortDF() and mixedSort() are na.last=TRUE so that default will be maintained for consistency.mixedSort() argument NAlast is deprecated in favor of na.last for consistency with base::sort().cPaste() was refactored to simplify internal logic, and to handle a rare edge case that was inconsistent with related functions. It occurs when the input list contains some factor vectors, and some non-factor vectors, and when both doSort=TRUE and keepFactors=TRUE. The keepFactors=TRUE argument tries to maintain factor levels during the sort, instead of using mixedSort() across all vectors. In this case, previously the non-factor vectors were converted to factor, which by default would order factor levels using sort(). Now the output is consistent in that the character vectors are converted to factors whose levels are ordered using mixedSort(). The step occurs once across all character vectors, so it is fairly fast even for large input lists. Also, any NULL entries are still maintained and returned as "".mixedSorts() was updated to allow input that has no names, which was errantly returning NULL. Now names are handled gracefully, allowing no names, or even duplicated names, without issue.mixedSorts() now properly handles nested list input that may contain NULL, so that it returns the same structured list including NULL entries where appropriate.uniques() new argument useSimpleBioc=TRUE will optionally enable Bioconductor SimpleList intermediate – mostly available to benchmark because it is so painfully slow it raised a red flag. The Bioconductor S4Vectors package changed how they handle List coersion from a simple list class, instead of using CompressedList it defaulted to use SimpleList. Unfortunately, SimpleList is roughly 6-10 times slower when calling unique(), and was causing curious slowdowns in other functions such as cPasteU. Bioconductor does not allow coersion directly to CompressedList, instead requires coersion by specific recognized classes such as "character" with "CharacterList", and "integer" with "IntegerList". So because the input list is allowed to contain different classes, the remedy is to make a CompressedList for each recognized class, call uniques() on that CompressedList, and repeat until all classes are handled. Any unrecognized classes are handled using lapply(x, unique). See examples for some benchmark comparisons. When useBioc=TRUE, the optimized Bioconductor method is used. When useBioc=FALSE, and useSimpleBioc=TRUE, the slower Bioconductor approach is used, which uses SimpleList as an intermediate. When both useBioc=FALSE and useSimpleBioc=FALSE, there are two additional options: keepNames=FALSE uses lapply(x, unique) and loses vector names; keepNames=TRUE will invoke a special base R approach that maintains the original vector names for the remaining unique entries. Of these four approaches the timings relative to the fastest:printDebug() has a new argument, largely silent, doReset which defines whether to apply an additional color reset to the delimiter argument sep. Previously the delimiter inherited the color from the previous text, but now by default the delimiter style is reset, giving more clear distinction between multiple values.printDebug() now properly applies the Crange and Lrange values when lightMode is TRUE, which means it limits the brightness of text colors on a light background, to ensure enough contrast to read the text. When using printDebugI() the background color is not adjusted, and the foreground (text) color is set using setTextContrastColor(), meaning either white or black depending upon the background brightness.setCLranges() and make_styles() were updated to apply options "jam.Crange", "jam.Lrange" only when those options were NULL, otherwise leave them as-is.applyCLrange() now properly applies the desired Crange and Lrange values, and defines the appropriate options, by default only when those options are NULL.fixYellow() default settings were changed to expand the range corrected “for green-ness”, also fixup=TRUE by default.hcl2col() argument was changed to fixup=TRUE, and model="hcl", consistent with other changes in color handling.hcl2col() and col2hcl() now use model="hcl" by default, which now calls the farver package if installed, otherwise they revert to using colorspace model="polarLUV" and fixup=TRUE. In future colorspace will likely be removed in favor of farver, so for now the transition has begun.setTextContrastColor() was adjusted to handle alpha transparency more accurately, the examples were updated and include a new example that uses drawLabels() on a dark background. New argument alphaLens allows some fine-tuning of the alpha transparency blending of foreground and background colors.shadowText() was updated to use several options() as default argument values. Although options() is not always an ideal mechanism, for purely visual effects it is not in conflict with statistical reproducibility, and allows some overall graphical settings to be maintained when shadowText() is being called through internal plot() functions. For example setting text <- jamba::shadowText then calling a default base R plot function will use the jamba::shadowText() in place of text(), but without allowing any customization. The options() mechanic allows some custom settings to be honored. The primary driver for these changes is in multienrichjam::jam_igraph() which plots igraph objects with some customization, one option is use_shadowText=TRUE which invokes jamba::shadowText(). It is desirable to adjust the contrast of the outline effect so it does not completely obscure the underlying network graph display.fix_matrix_ratio() is used to expand a matrix to have roughly 1:1 dimensions, up to a maximum factor per dimension. The purpose is to enhance image(), rasterImage(), and grid.raster() functions, specifically when interpolate=TRUE for images with more rows or columns than there are actual pixels to display the image. The interpolate=TRUE methods in base R do not account for assymetry, nor do they account for a low number of rows or columns. See examples for visible examples of the effect.The README.Rmd was re-organized, with more callouts of helpful jamba functions. Next step will be to include visual examples.
writeOpenxlsx() was exporting files with inconsistent word wrapping by column, and inconsistent vertical align (valign) settings. The culprit was openxlsx::saveWorkbook() which appears to apply default styles for cell styles that are not specifically encoded. Simply loading and saving a workbook would modify column styles. The workaround/fix was to ensure writeOpenxlsx() would specifically encode wrapText and valign for each cell, so that it would not be overridden by openxlsx::saveWorkbook() mood.writeOpenxlsx() now forces wrapText=TRUE for all columns. In future the function may allow per-column wrapText.applyXlsxCategorical() has new argument wrapText=TRUE which is passed to openxlsx::createStyle(), since that function requires wrapText be either TRUE or FALSE, and its default is FALSE.setTextContrastColor() no longer calls par("bg") to determine the background color, unless a graphics device is already open. This change will prevent a graphics device from being opened in somewhat random situations. The argument bg is only used when input colors have alpha transparency. When bg is not supplied, it will query par("bg") only when length(dev.list())>0, otherwise it uses "white" by default. Note that calling par() always opens a new graphics device if one is not already open, even though the "bg" value is stored somewhere and should not require a new device. The R docs do describe this behavior, for what it’s worth.imageByColors() now accepts argument cellnote as an atomic vector, which is coerced to a matrix with same dimensions as input matrix x. This change makes it easier to use numeric formatting functions, which sometimes take matrix input and provide vector output.applyCLrange() new argument fixup which is passed to hcl2col() which in turn passes it to colorspace::hex() when converting colors outside the color gamut. These functions will soon be replaced with calls to farver.hcl2col() and col2hcl() now have argument option model="hcl" that uses farver, and its color model "hcl", which is equivalent to using colorspace::hex(...,fixup=TRUE), except faster, and with better upside for other color manipulations. For now, the color model will not use "hcl" until I can work out better default values in colorjam::rainbowJam().rbindList() has two optional arguments:sdima() and ssdima() are equivalent to sdim() and ssdim() except that they operate on attributes(x). I somehow found myself constantly typing sdim(attributes(x)) and finally had enough of that.printDebugI() is a shortcut to printDebug(..., invert=TRUE), intended to be a quick way to use inverted colors, to colorize the background instead of the text. Note that printDebug() applies a color range restriction, to make sure the text contrasts with either light or dark background. When invert=TRUE the background color is not restricted, instead the foreground text uses setTextContrastColor() to determine a suitable contrasting color for the text and its corresponding background color.imageByColors() was refactored to handle grouped labels more cleanly. New argument groupByColors=TRUE decides whether to group cellnotes only when the label and underlying color are both identical – which is a change from previous behavior. Previous behavior grouped consecutive identical labels, regardless the underlying color, which is sometimes helpful, for example labeling a color gradient by the base color. Typically the cellnote and color would change together, but not always. The new default is consistent with the expected behavior.imageByColors() new argument groupBy with one or both values "row" which groups cellnote values by row, and "column" which groups cellnote values by column. Useful to limit cellnote grouping so the values are not grouped inappropriately. This argument is mostly useful when groupByColors=FALSE.imageByColors() new argument adjustMargins=TRUE will call adjustAxisLabelMargins() to adjust the margins to ensure the labels will fit in the plot device size.adjustAxisLabelMargins() was updated to handle par("cex") and par("cex.axis") appropriately.sdim() and ssdim() now handle environment input, or list of environments. Previously worked for sdim() but using random order returned by names(x) instead of proper order from ls(envir=x). An environment is essentially treated as a list, and ssdim() will now properly traverse into the environment as if it were a list.sdim() and ssdim() now handle "List" object classes and sub-classes from the S4Vectors Bioconductor package, but it only works when the S4Vectors package is previously loaded into the search path, otherwise the R object object system does not load the dependent package automatically. In that case, the slotNames(x) are used, which is somewhat less useful.imageDefault() now properly honors the par("bty") setting, that is by not calling its own box() to force drawing a box around the heatmap.make_styles() fixed issue with background color supplied in vector form, it was errantly calling fixYellow() with the logical vector of whether to colorize, instead of the color vector itself. This package needs "testthat".printDebug() now handles nested lists, calling jamba::unnestList() which flattens nested lists to one layer. This change allows printing a list printDebug(c("one", "two "), c("three", "four")) or l <- list(c("one", "two "), c("three", "four"));printDebug(l);.printDebug() now uses color2gradient() to create alternating light-dark shadings, used when a single color is defined for a multi-item vector concatenated by sep=",". The gradient was more reliable (so far) than makeColorDarker() because ANSI output is limited, as are the colors allowed for contrast with light or dark background.printDebug() new argument htmlOut=TRUE will output character string containing text colorized using HTML using the format <span style="color:red;background=white">text</span>. Intended whenever the colorized text would not otherwise be interpreted and colorized in a web browser context. It calls make_html_styles().make_html_styles() is a new function, which takes a vector of text, a vector of foreground colors, a vector of background colors, and returns a character string with HTML which colorizes the text. This function is intended for Rmarkdown or web page HTML output.jargs() was updated to handle arguments with vectors containing negative numbers. The negative - sign for example from -3 is being returned by formals() as call(\\-\, 3), which stores the numeric value separate from the negative sign. This seems like a change, which therefore broke how the colorization previously worked. For now the function works, but somehow lost the ability to colorize numeric vectors by value. Will leave for future.pasteByRow() properly handles leading blanks, it previously only correctly handled blank values in the second and subsequent columns. Caused by trying to simplify the R function when moving into the jamba package.plotPolygonDensity() new argument highlightPoints allows highlighting points in the distribution, which is currently displayed as histogram bars on top of the histogram and density polygon fill. Also slight change to how the polygon density is sized, it uses the median ratio of the height of the density curve to the histogram bars at the center of each bar.drawLabels() first argument is txt which is the label to be displayed, a small convenience change.breaksByVectors() examples were updated to fix a typo when calling adjustAxisLabelMargins().docs/articles for pkgdown.cPaste() default doSort=TRUE is changed to doSort=FALSE. New functions: cPasteS() is intended for sorted values; cPasteU() is an alias for cPasteUnique() and is intended for unique values; cPasteSU() is intended for sorted unique values. They all call cPaste() but with convenience defaults. It is recommended to use cPasteS() to replace sorted cPaste() in cases where output is expected to be sorted. The change was made now while impact is limited mostly to other Jam packages and could be mitigated.groupedAxis() draws grouped axis labels, a small convenience function that extends breaksByVectors().provigrep() when input is not character, the use of make.unique() requires explicit conversion to character type first.provigrep() was enhanced to handle duplicated input entries, which previously returned only the unique entries, but now correctly returns all entries including duplicates, in the proper order. The optional list output also makes each list element unique. New argument value allows returning index positions, which is equivalent to proigrep(). Lastly, the ignore.case argument is now properly honored, in order to allow case-sensitive matching.checkLightMode() will not try to use rstudio::getThemeInfo() if that package is installed, and if the function API exists, in order to determine whether Rstudio is currently using a dark theme.make_styles() has a new optional argument bg_style which allows defining the foreground style and background bg_style in one step. When bg_style is supplied, the Crange and Lrange arguments are ignored. Fixed a bug when rendering in Rstudio, where an ANSI foreground color of white does not get properly reset, causing all subsequent foreground colors to be white despite clear ANSI codes for different colors. The workaround is to render white as slightly off-white (greyscale 254 instead of 255) which restores correct output.printDebug() was enhanced to use the bg_style argument of make_styles(). New argument invert which will switch foreground and background colors. Fixed some follow-up issues with handling empty strings.cPaste() fixed issue with cPaste(NULL) and cPaste(list(NULL)) which previously caused an error, now returns "" consistent with output from cPaste(list(NULL, letters[1:2])) where NULL entries produce "".fixYellow() new argument fixup passed to hcl2col() which fixes out of gamut colors to scale within viewable range.writeOpenxlsx() was not properly saving rownames with argument keepRownames=TRUE, this issue was resolved.make_styles() where the default Lrange was getOption("jam.Crange") instead of getOption("jam.Lrange"). The affect is limited to debugging output when printed on a dark background.asSize() was updated to handle object_size above 2.1e9 (2 Gigabytes), it previously converted to integer which does not handle values that large, but now converts to numeric.log2signed() performs log2 transformation of the magnitude of the numeric values, while preserving the directionality. It effectively performs log1p(abs(x))*sign(x) except that by default it uses log base 2.exp2signed() is the reciprocal to log2signed(), it exponentiates the magnitude of the numeric values, while preserving the directionality.minorLogTicks().setTextContrastColor() default hclCutoff was changed from 73 to 60, in order to use dark text more often for the “in between” colors.makeNames() now uses duplicated() to detect duplicates prior to assigning names, which is substantially faster for long vectors where not all entries are duplicated, when compared to applying table(x) to the entire vector. For large vectors with mostly duplicated values, the speed is the same as before. Note this change also affects nameVector().sdim() now handles a special case of S4 object where data is stored in one slot with slotName ".Data", for example "limma::MArrayLM-class" uses this format. When the length of names(x) matches the length of slot(x, ".Data") then those names are applied.sclass() now properly detects S4 objects, and specifically recognizes data.frame as a list even though it secretly has slotNames like an S4 object, while not being an S4 object. (Is it?) Matrix-like objects return the class of each column for consistency, even though all columns have identical class. This function also handles the same special case S4 scenario when it has only one slotName ".Data", as described above for sdim().mixedOrder() did not sort properly when any entry contained only "-" dashes, this problem has been fixed. Previously “-” was potentially used to indicate negative numbers and therefore not treated as a blank value, inadvertently becoming NA and disrupting the ordering. Now strings "-" and "---" are considered blanks.
mixedOrder() now uses the input string as a final tiebreaker, so blank strings like "--" and "-" will also be sorted c("-", "--") in the output instead of returning in the same order as the input.
mixedOrder(), several regular expressions were updated to cover edge cases, and will soon be wrapped into a series of "testthat" unit tests, long overdue. Also, verbose output was slightly updated. Specifically:
blanksFirst=TRUE, and at the end when blanksFirst=FALSE.NAlast=FALSE and NAlast=TRUE respectively. The NA order has priority over blanks, so NA will always be completely first or completely last.keepInfinite=TRUE will be ordered at the end, but before blanks, then before NA values, if those values are also positioned at the end. Also, when keepNegative=TRUE then "-Inf" will be position at the beginning, but after NA then after blanks, if those values are also positioned at the beginning.keepNegative=TRUE also enables recognition of scientific notation, but that regular expression wrongly allowed decimal exponentials, which is not valid (e.g. “1.23e1.2” is not valid.) now the exponential only includes non-decimal numeric values, e.g. "-1.23e2.2" is effectively considered "-1.23e2" and "2".mixedSort(), mixedSorts() and mixedSortDF() are all affected by the changes to mixedOrder().
mixedSorts() was updated to enable correct behavior when sortByName=TRUE, which only works when all vectors in the input list are named.
mixedSorts() will accept nested lists, and would have used the ultra-cool utils::relist() function, except that function does not allow re-ordering the vector names within the nested list. So a new function relist_named() was added to jamba. It also works with sortByName=TRUE to sort each vector by its names, by only if all vectors are named.
relist_named() is a small modification of the utils::relist() generic function (actually mostly just the utils:::relist.default()). This function splits a vector into a list matching the structure of a skeleton list, except that the names of each vector in the output list will match the input vector x and not the names from the vectors in the skeleton list.cPaste() now properly handles a list with factor and non-factor types, previously base::unlist() coerced the mixed list to character which changed factor values to integers when non-factor elements were present. Now keepFactors=TRUE will preserve factor levels when sorting with doSort=TRUE.gsubOrdered() applies base::gsub() to character or factor input, and returns a factor output, retaining the order of levels based upon the input.jargs() changed the default sortVars=FALSE which prints function arguments in the order they are defined.mergeAllXY() merges multiple data.frames, keeping all rows and columns.unnestList() flattens a nested list-of-lists into a simple, flat list.makeColorDarker() fixed issue with repeated colors and darkFactors, processed using unique combination of color,darkFactor,sFactor to improve efficiency with large vectors, but was not properly handling the unique vectors.uniques()
col2hcl() uses colorspace::sRGB() instead of colorspace::RGB() to match the convention that colorspace::hex2RGB() actually uses sRGB and not RGB as the function name (and all common sense in the realm of how to name a function) implies.col2hcl() and hcl2col() allow selecting from polarLUV or polarLAB color models, both of which use HCL values to generate colors.col2hcl() no longer forces the output vector to have names, however it retains names if provided in the input.hcl2col() will use polarLUV or polarLAB as input without converting to an intermediate color space, which makes output slightly less lossy than converting to and from sRGB.ucfirst() is a simple function to uppercase the first letter in a word or phrase.mixedSorts() will sort a list of vectors using mixedSort() alphanumeric sort, and fairly efficiently too! It sorts the unlisted data then splits it back to a list.drawLabels() and coordPresets() were moved from the jamma package. The drawLabels() can be used to add text labels to a plot, with convenient coordinate presets handled by coordPresets() which include things like “topleft”, “center”, or “right”. It automatically adjusts the text position to stay inside the plot border in those cases.writeOpenxlsx() is a wrapper for the openxlsx package, intended to encapsulate a large number of default options for certain “known” column data types, like P-values, log2 fold changes, and integer values.applyXlsxCategoricalFormat() and applyXlsxConditionalFormat() to apply colors to an existing Excel xlsx file worksheet. These functions are called by writeOpenxlsx() but can also be called manually to customize an existing Excel file.setTextContrastColor() has been updated to handle alpha transparency, semi-transparent colors are blended with the background color, then compared to the threshold.formatInt() is a quick wrapper function to format numeric values as integers, by default rounding decimal values and using big.mark=“,”, which can be overridden as needed.list2df() to convert a list of vectors into a tall data.frame.warpAroundZero() was not properly handlingbaseline`, the method now uses a more straightforward approach.pasteByRowOrdered() is an extension to pasteByRow() which creates an ordered factor, where the individual column order is maintained, either using existing factor level ordering, or via mixedSort() per column.unalpha() simply removes the alpha transparency from an R hex color, which is required for some plotly functions for example.isTRUEV() and isFALSEV() are vectorized forms of isTRUE() and isFALSE(). As they take vector input, the entire vector must be logical in order for any entry to be considered.rgb2col() was enhanced so the alpha argument conveys whether to return alpha transparency in the output string. It seemed to be a convenient place to control alpha since the conversion of color names to hex requires converting to RGB as an intermediate, then back to hex color.minorLogTicks() and minorLogTicksAxis() had an argument renamed to offset instead of labelValueOffset. Better to change it now before it has wider use. Also, the defaults were changed to logBase=2 and displayBase=10 based upon the current most frequent usage. Best to set these values explicitly. Ideally, R graphical parameters should define the log base instead of TRUE/FALSE in par("xlog") and par("ylog").normScale() was modified so the low and high range values are properly honored even when supplying a single value for x. Now the behavior checks if low is equal high to determine whether to use the low and high values. This adjustment helps applyCLranges() restrict colors to allowed ranges without over-correcting single colors to the midpoint of the range.sqrtAxis() which computes axis tick mark positions for data that has been square root transformed, using transformation sqrt(abs(x))*sign(x) in order to maintain positive and negative values. This function is called by plotPolygonDensity() when using xScale="sqrt".getColorRamp() with RColorBrewer colors, where it previously would retrieve colors using a number higher then the actual number supplied by RColorBrewer::brewer.pal(), and which only issues a warning (which I had hidden.) The code now checks for the proper maximum number, and expands to the larger number using colorRampPalette() as needed.cPaste() to handle lists with a single NA value, which failed previously because a single NA is considered class “logical” and not “character” as required by S4Vectors::unstrsplit().Crange and Lrange values are used in make_styles(), the new default will not overwrite the global Crange and Lrange settings.Crange and Lrange values are enforced by applyCLranges(). There is a new argument CLmethod which controls how C and L values are adjusted.fillBlanks() is used to fill a vector that has missing values, and fills missing values with the most recent non-blank value. It is useful when importing Excel data where headings might be present in the first cell of a block of cells, followed by blanks.newestFile() takes a vector of files, and returns the most recently modified, using file.info().grepls() a useful utility for search the active environment by object name. For example grepls("statshits") will find everything named “statshits”, or grepls("farris") will find everything with “farris” in the name”, even within packages, or other attached environments in the search space.warpRamp() takes a vector of colors as from a color gradient, and warps the gradient. For divergent colors, the adjustmet is symmetric around the middle color; otherwise the adjustment is relative to the first color. Helpful for adjusting colors scales in heatmaps.imageDefault(), plotSmoothScatter(), smoothScatterJam() were updated to allow values lower than 200 for nbin which previously caused problems when fixRasterRatio=TRUE and oldstyle=TRUE.rmNA() by default returns NULL when given NULL input, unless nullValue is defined. This change fixed several warnings, and resolved inconsistencies with setCLranges() not handling NULL parameters properly, consequently affecting make_styles() ability to restrict the color chroma (C) and luminance (L) ranges, seen when printDebug() did not use scaled colors.hcl2col() during detection of RGB values above 255, which sometimes happens during the colorspace::polarLUV() conversion from HCL to RGB.rlengths() returns the recursive lengths of list elements, intended when a list may have multiple nested lists. It returns the top level of counts per list element by default, but with doSum=FALSE it returns the full structure with the length of each non-list element.minorLogTicksAxis() and minorLogTicks() provide log-transformed axis labels, with the added benefit of handling log(1+x) transformations properly; or log2FoldChange data with symmetry around zero.renameColumn() a basic function but which allows re-running the function without error.normScale() scales a numeric vector into a fixed range, by default between 0 and 1. If one value is given, a parameter singletMethod defines whether to use the minimum, maximum, or mean of the range.rowGroupMeans() and rowRmMadOutliers() are used to compute per-row mean values, with grouped columns. Optional outlier detection is performed using a MAD factor cutoff, for example 5xMAD threshold means points 5 times the MAD for the group are considered outliers.plotPolygonDensity() which is a wrapper around hist() and plot(density(x)), but with some added features like scaling the x-axis by log10 or sqrt; and multi-panel output when the input is a multi-column matrix.warpAroundZero() takes a numeric vector, and warps the values with a log curvature, symmetric around zero. The intent is to create non-linear breaks when used in heatmaps with divergent color ramps.ssdim() was updated again to try to handle more non-list object types, for example the “bga” class returned from made4::bga().%>% inside \code{\%>\%} blocks, which allows the percent sign to be escaped and ignored.\code{\link{}} sections which did not properly specify the package name. The issue apparently only causes errors during package install on systems using HTML as the preferred help format.smoothScatterJam() and imageDefault() were updated to fix edge cases where the image being rendered was expected to have integer axis units, but where the raster ratio had duplicated columns or rows, making the units imprecise.setPrompt() has default projectName=NULL instead of trying to pull from projectName from the .GlobalEnv environment, which would cause an error if not defined. Instead, if NULL then it checks if projectName exists, if so the value is used.sdim() so it would properly traverse a non-vector and non-list object which may contain elements with length or dimension.setCLranges() was adjusted to use global options where available, and by default will update global options when not defined. This mechanism allows one to set specific Crange and Lrange values, and have them be re-used by functions affected by those values.ssdim() now handles S4 objects by iterating each slotName and calling sdim().sdim() now properly handles detection of S4 classes.fixYellowHue() takes a matrix of HCL colors (as from col2hcl()) and adjusts colors between hue 80 and 90 so they appear less green. This change is a visual preference that the default yellow appears green when darkened, and simply makes the color appear less green.fixYellowColor() takes a vector of colors as a wrapper to fixYellowHue().cPaste() is an efficient method of pasting a list of vectors using a delimiter, to create a character vector. It uses mixedOrder() to sort entries, and optionally applies uniqueness to the vectors.uniques() takes a list and makes each vector in the list unique, using an efficient mechanism that applies uniqueness to the overall set of values at once.S4Vectors implements efficient unstrsplit() used by cPaste(). However, S4Vectors therefore requires installing Bioconductor base packages, which might be a heavy installation requirement just for improved efficiency at this step. In future this one function may be reproduced here (with permission of author Dr. Pages) to reduce the dependency burden.jargs() does a better job of handling functions with nested lists, and closes any open [ with corresponding ].jargs() properly honors useColor=FALSE to disable colorized text, and adds colNULL to assign a color for NULL values, by default grey.printDebug(), make_styles() will apply a CL range, chroma (C) and luminance (L) values, which are defined in part by lightMode and corresponding function checkLightMode(), and a helper function setCLranges() which sets sensible default values for light and dark backgrounds.printDebug() has two optional parameters Crange and Lrange which define a chroma (C) range and luminance (L) range. For lighter background, a maximum luminance of 80 seems reasonable; for darker background colors, minimum luminance of 75 is effective. The only awkwardness is that yellow darkens to a greenish hue, which is not aesthetically pleasing, so because I even noticed it, I had to “fix” the issue by adjusting yellows to more gold before darkening, enabled with default argument fixYellow=TRUE.make_styles() calls applyCLrange() which fixes the chroma (C) and luminance (L) values, hopefully to sensible default values.applyCLrange() takes a vector of colors, and fixes the chroma (C) and luminance (L) values to this range. If Cgrey is above zero, then colors with chroma (C) value below this threshold are kept unchanged, in order to prevent a purely grey (unsaturated) color from becoming colorized.setCLranges() will query checkLightMode() and return Crange and Lrange default values.hcl2col() which simply converts the output of col2hcl() back to a vector of R hex colors. It should not be lossy, meaning it should faithfully convert R colors to an HCL matrix, then back to the same R original hex colors. Alpha transparency is also maintained. Note that hcl2col() performs differently than grDevices::hcl() which does not produce the same colors as colorspace::polarLUV(H, C, L) using the same values for H, C, and L. The reasons unclear, however the functions in jamba are internally consistent, using colorspace functions.jam.adjustRgb - numeric, sets the parameter “adjustRgb” in printDebug().jam.lightMode - boolean, sets the lightMode, see below.printDebug() has a new boolean parameter “lightMode”, which is TRUE when the background color is light (e.g. white or light-grey.) In this case, it applies a ceiling to the brightness of all text colors to ensure none are too bright to be visible.mixedSortDF() now accepts character values for byCols, with optional prefix “-” to indicate decreasing sort. Alternatively, the parameter decreasing will still be used to reverse the sort, and is converted to a vector when byCols has multiple values. Note that the prefix “-” and decreasing are multiplied to combine them.smoothScatterJam() tests if postPlotHook is a function, in which case it runs postPlotHook(...) otherwise it simply evaluates postPlotHook;
nullPlot(), usrBox(), and imageDefault() have a new boolen parameter “add” indicating whether to create a new plot or add to an existing plot device.rbindList() has a new boolean parameter keepNA indicating whether to keep NA values in the results, which ultimately causes NA to be converted to “NA”.makeNames() has a new boolean parameter keepNA indicating whether to keep NA values in the results. When keepNA is TRUE, NA is converted to “NA”, otherwise NA entries are treated as “” prior to creating names.rmNA() changed the default value for parameter rmNAnames to FALSE, which was the more anticipated behavior. An input vector will not be shortened for non-NA values that have an NA name. Changing function parameter defaults will be an extremely rare occurrence in future.make_styles() which is a vectorized wrapper for crayon::make_style(), gains some finer control over color chroma and luminance.jargs() gets a larger refactoring, aimed at better display of list parameters, and lists of lists and other nested variations. It now does a better job of displaying the list and vector names appropriately. A new function handleArgsText() was split into a separate function, but is a rare non-exported function since it is currently only useful for jargs().applyLceiling() intended to restrict colors to a maximum luminance in HCL color space, mainly to support the new lightMode option intended for using printDebug() with a light background.checkLightMode() intends to support the new lightMode option by doing its best to check situations to enable lightMode. It first checks options(“lightMode”). It then checks environment variables that suggest Rstudio is running, in which case it defaults to lightMode=TRUE, since the default Rstudio has a light background.sclass(), sdim(), and ssdim() are intended to help handle list objects.
sclass() returns the class of each list element.sdim() returns the dimensions (or lengths) or each list element.ssdim() is a special case that returns the dimensions of a list of list of objects. In all cases, if the input object is an S4 object, it operates on slotNames(x). Thus, calling ssdim(x) is helpful for S4 objects, since it returns the class and dimensions of each object inside the S4 object.