minorLogTicks() R function from [jamba]

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", "flip", "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.
col, col.ticks: character color used for the axis label, and axis tick marks, respectively, default "black".
combine: logical, default FALSE, whether to combine major and minor ticks into one continuous set of major tick marks.
logAxisType: character string indicating the type of log axis:
- normal: typical axis style and orientation
- flipped: used for reverse orientation
- pvalue: used for -log10(pvalue) orientation.
verbose: logical indicating whether to print verbose output.
...: additional parameters are ignored.

Returns

list of axis tick positions, and corresponding labels, for major and minor ticks. Note that labels may be numeric, character, or expression. Specifically when expression

the graphics::axis() must be called once per label.

majorTicks: numeric position of each major tick mark
minorTicks: numeric position of each minor tick mark
allTicks: numeric position of each major tick mark
majorLabels: label to show for each tick mark
minorLabels: label to show for each tick mark
minorSet: the numeric steps requested for minor ticks
minorWhich: the numeric steps requested for minor labels
allLabelsDF: data.frame with all tick marks and labels, with colname "use" indicating whether the label is displayed beside each tick mark.

Details

This function is called by minorLogTicksAxis(), and it may be better to use that function, or logFoldAxis()

or pvalueAxis() which has better preset options.

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, which 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).

Motivation

This function is motivated to fill a few difficult cases:

Label axis ticks properly when used together with offset. For example log2(1 + x)

uses offset=1. Other offsets can be used as relevant.
Create 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.
Use symmetric tick marks around x=0 when applied to log fold changes.
Display actual P-values when plotting log10(Pvalue), which is common for volcano plots.

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$allLabelsDF, type %in% "major");
graphics::axis(1, las=2,
   at=maj$tick, label=maj$text);
min <- subset(mlt$allLabelsDF, type %in% "minor");
graphics::axis(1, las=2, cex.axis=0.7,
   at=min$tick, label=min$text,
   col="blue");
graphics::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);
abline(v=0, lty=2)
graphics::axis(3, las=2);
minorLogTicksAxis(1, logBase=2, displayBase=10, symmetricZero=TRUE);

nullPlot(xlim=c(-4,10), doMargins=FALSE);
graphics::axis(3, las=2);
minorLogTicksAxis(1, logBase=2, displayBase=10, offset=1);
x2 <- stats::rnorm(1000) * 40;
d2 <- stats::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);
graphics::axis(3, las=2);
minorLogTicksAxis(1, logBase=2, displayBase=10, offset=1);
x1 <- c(0, 5, 15, 200);
graphics::text(y=rep(1.0, 4), x=log2(1+x1), label=x1, srt=90, adj=c(0,0.5));
graphics::points(y=rep(0.95, 4), x=log2(1+x1), pch=20, cex=2, col="blue");

minorLogTicks function