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Render venndir output

Source: R/venndir-render-jp.R
render_venndir.Rd

Render venndir output

Usage

render_venndir(
  venndir_output = NULL,
  expand_fraction = NULL,
  font_cex = 1,
  main = NULL,
  item_cex = NULL,
  item_cex_factor = 1,
  plot_warning = FALSE,
  show_labels = NULL,
  show_items = NULL,
  item_degrees = NULL,
  max_items = 100,
  show_zero = TRUE,
  show_segments = NULL,
  segment_buffer = NULL,
  label_preset = c("none"),
  label_style = c("custom", "basic", "fill", "shaded", "shaded_box", "lite", "lite_box"),
  fontfamily = NULL,
  inside_percent_threshold = 0,
  item_style = NULL,
  item_buffer = NULL,
  group_labels = TRUE,
  template = NULL,
  adjust_center = FALSE,
  draw_legend = NULL,
  legend_x = "bottomright",
  legend_font_cex = NULL,
  show_label = NA,
  display_counts = TRUE,
  do_newpage = TRUE,
  do_draw = TRUE,
  draw_buffer = FALSE,
  verbose = FALSE,
  debug = FALSE,
  ...
)

Arguments

venndir_output

Venndir output from venndir(), or list with element "vo" as a Venndir object.

expand_fraction

numeric value, default NULL to use automated settings. It defines the figure margin fraction on each side in order: bottom, left, top, right. The default settings:

  • When draw_legend=FALSE it uses c(0, 0, 0, 0).

  • When draw_legend=TRUE it uses c(0.18, 0, 0, 0), in order to help prevent the Venn diagram from overlapping the legend.

  • When expand_fraction is defined, it is used without any adjustment.

font_cex

numeric scalar to adjust font sizes.

main

character string used as a plot title, default NULL will render no title. When provided, it is rendered using gridtext::richtext_grob() which enables some Markdown-style formatting. The title is stored in venndir@metadata$main for persistence.

item_cex

numeric default NULL, used to define baseline font size (single value), or exact font cex values (multiple values).

  • When a single value is provided, each set of items is used to define a font scaling, based upon the relative area of the overlap polygon to the max item polygon area, and the number of items in each polygon. These values are multiplied by item_cex to produce the final adjustment. These values are multiplied by item_cex_factor.

  • When multiple values are provided with names, the names are matched with overlap names: venndir_output@label_df$overlap_set, and applied accordingly. Any missing values retain the pre-existing value by default.

  • When multiple values are provided without names, the length is matched to the number of polygons in venndir_output@jps@polygons with non-zero and non-NA venn_counts; or the number of unique polygons in venndir_output@jps@polygons$venn_name; or the number of unique overlaps in venndir_output@label_df$overlap_set. If a length match is found, those values are assigned to names(item_cex). There is no further adjustment by polygon area, nor number of labels. These values are multiplied by item_cex_factor.

item_cex_factor

numeric, default 1, used to adjust the item_cex values overall. It is intended to be a single value, and is multiplied by item_cex as it is defined for each set of items.

plot_warning

logical indicating whether to include a warning when one or more non-zero overlap counts cannot be displayed in the figure. Not yet re-implemented since version 0.0.30.900.

show_labels

character string to define the labels to display, and where they should be displayed. The definition uses a single letter to indicate each type of label to display, using UPPERCASE to display the label outside the Venn shape, and lowercase to display the label inside the Venn shape. The default "Ncs" displays _N_ame (outside), _c_ount (inside), and _s_igned count (inside).

The label types are defined below:

  • _N_ame: "n" or "N" - the set name, by default it is displayed.

  • _O_verlap: "o" or "O" - the overlap name, by default it is hidden, because these labels can be very long, also the overlap should be evident in the Venn diagram already.

  • _c_ount: "c" or "C" - overlap count, independent of the sign

  • _p_ercentage: "p" or "P" - overlap percentage, by default hidden, but available as an option

  • _s_igned count: "s" or "S" - the signed overlap count, tabulated based upon overlap_type ("each", "concordant", "agreement", etc/)

  • _i_tems: "i" only, by default hidden. When enabled, item labels defined by show_items are spread across the specific Venn overlap region.

show_items

character used to define the item label, only used when the show_label entry includes "i" which enables item display inside the Venn diagram.

  • "item": shows only the item labels

  • "sign": shows only the sign of each item

  • "sign items": shows the sign and item together (or "item sign" will show the item, then the sign).

item_degrees

numeric angle (default 0) in degrees used to adjust item label display.

max_items

numeric (default 3000) indicating the maximum number of item labels to display when enabled.

show_zero

logical (default FALSE) indicating whether empty overlaps are labeled with count zero 0. When show_zero=TRUE the count zero label is displayed, otherwise no count label is shown.

show_segments

logical (default TRUE) indicating whether to draw a line segment from the Venn region to any label positioned outside.

segment_buffer

numeric (default -0.1) indicating the depth inside each Venn region a line segment will be drawn, relevant only when show_segments=TRUE.

label_preset

character deprecated in favor of show_labels. This argument is passed to venndir_label_style().

label_style

character string indicating the style for labels. Label color is adjusted based upon the determined background color, determined based upon the label fill color, and either the device background color, or Venn overlap fill color. There are pre-defined label styles.

  • "basic" no background shading

  • "fill" an opaque colored background

  • "shaded" a partially transparent colored background

  • "lite" a partially transparent lite background

  • "box" adds a dark border around the label region

fontfamily

character string to define the fontfamily. Default is "sans" because it should get mapped to a supported font for each graphics device. The fontfamily must match a recognized font for the given output device, and this font must be capable of producing UTF-8 / Unicode characters, in order to print up arrow and down arrow. You may review systemfonts::system_fonts() for a listing of fonts recognized by ragg devices, which seems to have the best overall font capabilities. When it does not work, either use unicode=FALSE, or check the output from Sys.getlocale() to ensure the setting is capable of using UTF-8 (for example "C" may not be sufficient). Using the package ragg appears to be more consistently successful for rasterized output than base R output, for example: ragg::agg_png(), ragg::agg_tiff(), ragg::agg_jpeg() produce substantially higher quality output, and with more successful usage of system fonts, than png(), tiff(), and jpeg(). Similarly, for PDF output, consider cairo_pdf() or Cairo::CairoPDF() instead of using pdf().

inside_percent_threshold

numeric (default 0) indicating the percent area that a Venn overlap region must contain in order for the count label to be displayed inside the region, otherwise the label is displayed outside the region. Values are expected to range from 0 to 100.

item_style

character string (default "text") indicating the style to display item labels when they are enabled.

  • "default" detects whether item labels contain "<br>" for newlines, and uses "gridtext" if that is the case, otherwise it uses "text" which is markedly faster.

  • "text" option is substantially faster, but does not allow markdown.

  • "gridtext": substantially slower for a large number of labels, but enables use of limited markdown by calling gridtext::richtext_grob(). Mostly useful for venn_meme().

item_buffer

numeric value (default -0.15) indicating the buffer adjustment applied to Venn overlap regions before arranging item labels. Passed to label_fill_JamPolygon() via render_venndir(). Negative values are recommended, so they shrink the region.

group_labels

logical (default TRUE) indicating whether to group label components together, therefore drawing fill and border around the group instead of each component. In most cases this setting should be TRUE.

template

character (default "wide") describing the default layout for counts and signed counts. The value is stored in venndir@metadata$template for persistence.

  • "wide" - main counts on the left, right-justified; signed counts on the right, left-justified.

  • "tall" - main counts, center-justified; signed counts below main counts, center-justified.

adjust_center

logical (default TRUE) used when labels are grouped, whether the group should be re-centered on the target point. Try adjust_center=FALSE if wide label groups are adjusted so that the count label is too far left.

draw_legend

logical (default NULL) indicating whether to draw a legend, calling venndir_legender(). When NULL it uses metadata(venndir_output)$draw_legend when defined, otherwise defaults to TRUE.

legend_x

character passed to venndir_legender() to customize the position of the legend.

legend_font_cex

numeric scalar to adjust the legend font size.

do_newpage

logical (default TRUE) indicating whether to call grid::grid.newpage(). This option allows the figure to be rendered inside an active display device, or active grid::viewport. Note: When do_draw=FALSE, it also forces do_newpage=FALSE.

do_draw

logical indicating whether to call grid::grid.draw(). The grid graphical objects are returned in attributes: "gtree", "grob_list", "viewport", and can be drawn separately.

verbose

logical indicating whether to print verbose output.

debug

numeric optional internal debug.

...

additional arguments are passed to internal functions.

Value

Venndir object with attributes that contain underlying grid graphical objects (grobs):

  • "gtree": a grid::gTree object suitable for drawing with grid::grid.draw(attr(vo, "gtre"))

  • "grob_list": a list of grid object components used to build the complete diagram, they can be plotted individually, or assembled with do.call(grid::gList, grob_list). The grid::gList can be assembled into a gTree with: grid::grobTree(gList=do.call(grid::gList, grob_list)

  • "viewport": the grid::viewport that holds important context for the graphical objects, specifically the use of coordinate grid::unit measure "snpc", which maintains a fixed aspect ratio.

Details

About fonts and unicode symbols

R handles unicode symbols for each graphics device somewhat independently. Creating a PNG uses a different set of fonts than creating a PDF. Not all fonts used for PNG are compatible with PDF, and vice versa. (It is not solely an R problem.)

For the most part, users should not have to care about these details...

How this affects venndir:

Not every font registered in R supports extended unicode characters upArrow and downArrow, which causes it to draw blank boxes like []. The quick options:

  • Try a different fontfamily that may support the characters of interest.

  • Try a different grob type, see text_grob_type="marquee" below.

  • Install extrafont, which may be useful for installing consistent fonts to be used with PNG and PDF output formats.

Additional options

Several options are passed through ... (ellipses) to internal functions, documented below:

  • L_threshold is passed to make_color_contrast() and controls the _L_uminance at which text is either dark or light.

  • text_grob_type is passed to assemble_venndir_labels() and controls the text grid graphical object (grob) type used. Note that "marquee" requires the marquee package, which implicitly requires R-4.3 or newer, though somehow that is not a formal dependency. R-4.3 adds glyph rendering, which is required by marquee.

    • text_grob_type="textGrob" (default) uses grid::textGrob() which only handles text, and no markdown. It is also fastest.

    • text_grob_type="richtext_grob" uses gridtext::richtext_grob(), and requires the gridtext package. It handles a subset of markdown (bold, italics, but not bullets), and a subset of HTML markup such as inline CSS styles. It sometimes produces visual glitches, where whitespace between words can be inconsistent, otherwise it would have been the default.

    • text_grob_type="marquee" uses marquee::marquee_grob(), which requires the marquee package. It may rarely cause a full R crash on MacOS, apparently due to font handling subsystems, otherwise it would have been the default. Its rendering of Unicode is outstanding, since it uses systemfonts to substitute any missing glyphs per font, for example the upArrow/downArrow symbols. It handles full markdown, including bullets, but not tables, nor HTML. It does not support table format, through version 0.1.0, however.

  • fontfamilies is passed to assemble_venndir_label(), as a list with three named elements: "overlap", "count", "signed".

    • The fontfamily can be customized for each element, which may be useful for a custom font for the overlap label, and a different font (e.g. one that contains upArrow/downArrow unicode characters) for the count and signed count labels.

    • The custom font is also accepted by venndir_legender() for consistency.

  • outerborder,outerborder.lwd,innerborder,innerborder.lwd, border,border.lwd - these arguments are passed to plot.JamPolygon() and override internal values when defined. They can be used to produce interesting visual variations of the Venn diagram. For example:

    • outerborder.lwd=0, innerborder.lwd=0, border="white", border.lwd=3 will use a white border.

    • outerborder.lwd=0, innerborder.lwd=4, border="white", border.lwd=1 will use a wide internal border, and thin white line between overlaps.

See also

Other venndir core: signed_overlaps(), textvenn(), venn_meme(), venndir()