Calculate major and minor tick marks for log-scale axis

Calculate major and minor tick marks for log-scale axis

minorLogTicks(
  side = NULL,
  lims = NULL,
  logBase = 2,
  displayBase = 10,
  logStep = 1,
  minorWhich = c(2, 5),
  asValues = TRUE,
  offset = 0,
  symmetricZero = (offset > 0),
  col = "black",
  col.ticks = col,
  combine = FALSE,
  logAxisType = c("normal", "flipped", "pvalue"),
  verbose = FALSE,
  ...
)

Arguments

side

integer value indicating which axis to produce tick marks, 1=bottom, 2=left, 3=top, 4=right.

lims

numeric vector length=2, indicating specific numeric range to use for tick marks.

logBase

numeric value indicating the logarithmic base, assumed to be applied to the numeric lims limits, or the axis range, previously.

displayBase

numeric value indicating the base used to position axis labels, typically displayBase=10 is used to draw labels at typical positions.

logStep

integer value indicating the number of log steps between major axis label positions. Typically logStep=1 will draw a label every log position based upon displayBase, for example displayBase=10 and logStep=1 will use c(1,10,100,1000); and displayBase=10 and logStep=2 would use c(1,100,10000).

minorWhich

integer vector of values to label, where those integer values are between 1 and displayBase, for example displayBase=10 may label only c(2,5), which implies minor tick labels at c(2, 5, 20, 50, 200, 500). Any minor labels which would otherwise equal a major tick position are removed. By default, when displayBase=2, minorWhich=c(1.5) which has the effect of drawing one minor label between each two-fold major tick label.

asValues

logical indicating whether to create exponentiated numeric labels. When asValues=FALSE, it creates expression objects which include the exponential value. Use asValues=FALSE and logAxisType="pvalue" to draw P-value labels.

offset

numeric value added during log transformation, typically of the form log(1 + x) where offset=1. The offset is used to determine the accurate numeric label such that values of 0 are properly labeled by the original numeric value.

symmetricZero

logical indicating whether numeric values are symmetric around zero. For example, log fold changes should use symmetricZero=TRUE which ensures a log2 value of -2 is labeled -4 to indicate a negative four fold change. If symmetricZero=FALSE a log2 value of -2 would be labeled 0.0625.

verbose

logical indicating whether to print verbose output.

...

additional parameters are ignored.

Value

list of axis tick positions, and corresponding labels, for major and minor ticks. Major ticks are defined as one tick per log unit exponentiated. For example, 1, 10, 100, 1000 when displayBase=10.

Details

This function calculates log units for the axis of an existing base R plot. It calculates appropriate tick and label positions for major steps, which are typically in log steps; and minor steps, whic are typically a subset of steps at one lower log order. For example, log 10 steps would be: c(1, 10, 100, 1000), and minor steps would be c(2, 5, 20, 50, 200, 500, 2000, 5000).

This function was motivated in order to label log-transformed data properly in some special cases, like using log2(1+x) where the resulting values are shifted "off by one" using standard log-scaled axis tick marks and labels.

Also, when using log fold change values, this function creates axis labels which indicate negative fold change values, for example -2 in log2 fold change units would be labeled with fold change -4, and not 0.0625 which represents a fractional value.

Use the argument symmetricZero=TRUE when using directional log fold change values.

See also

Other jam practical functions: breakDensity(), checkLightMode(), check_pkg_installed(), colNum2excelName(), color_dither(), diff_functions(), exp2signed(), fileInfo(), fixYellow(), getAxisLabel(), handleArgsText(), heads(), isFALSEV(), isTRUEV(), jamba, jargs(), kable_coloring(), lldf(), log2signed(), make_html_styles(), make_styles(), match_unique(), mergeAllXY(), middle(), newestFile(), printDebug(), renameColumn(), rmInfinite(), rmNAs(), rmNA(), rmNULL(), sclass(), sdim(), setPrompt()

Examples

## This example shows how to draw axis labels manually,
## but the function minorLogTicksAxis() is easier to use.
xlim <- c(0,4);
nullPlot(xlim=xlim, doMargins=FALSE);
mlt <- minorLogTicks(1,
   logBase=10,
   offset=1,
   minTick=0);
maj <- subset(mlt$allLabelsDF, type %in% "major");
axis(1, las=2,
   at=maj$tick, label=maj$text);
min <- subset(mlt$allLabelsDF, type %in% "minor");
axis(1, las=2, cex.axis=0.7,
   at=min$tick, label=min$text,
   col="blue");
text(x=log10(1+c(0,5,50,1000)), y=rep(1.7, 4),
   label=c(0,5,50,1000), srt=90);


nullPlot(xlim=c(-4,10), doMargins=FALSE);
axis(3, las=2);
minorLogTicksAxis(1, logBase=2, displayBase=10, symmetricZero=TRUE);


nullPlot(xlim=c(-4,10), doMargins=FALSE);
axis(3, las=2);
minorLogTicksAxis(1, logBase=2, displayBase=10, offset=1);
x2 <- rnorm(1000) * 40;
d2 <- density(log2(1+abs(x2)) * ifelse(x2<0, -1, 1));
lines(x=d2$x, y=normScale(d2$y)+1, col="green4");


nullPlot(xlim=c(0,10), doMargins=FALSE);
axis(3, las=2);
minorLogTicksAxis(1, logBase=2, displayBase=10, offset=1);
x1 <- c(0, 5, 15, 200);
text(y=rep(1.0, 4), x=log2(1+x1), label=x1, srt=90, adj=c(0,0.5));
points(y=rep(0.95, 4), x=log2(1+x1), pch=20, cex=2, col="blue");