heatmapOptions: Generate default options for a Heatmap

In mgperry/heatmaps: Flexible Heatmaps for Functional Genomics and Sequence Features

Description

Generate default options for a Heatmap

Usage

heatmapOptions(...)

Arguments

...

options to set manually Guide to Heatmap options This is an reference to all the possible options for plotting heatmaps. Some options are handled by heatmaps functions (either plotHeatmap or plotHeatmapList), others are passed directly to plotting functions. Further explanation is available in the vignette. Arguments are numeric if not otherwise stated. color: A vector of colors or a default color, see ?default_color. plotHeatmap will interpolate between these colors to form a scale. box.width: width of box around the heatmap, passed to box() x.ticks: Logical, plot x axis ticks x.tick.labels: Character, labels to use for x ticks, (default blank) tcl: Length of x axis ticks padj: Vertical adjustment of x axis labels cex.axis: cex for axis labels scale: Logical, Plot scale or not scale.label: Character, label for scale scale.lwd: Width for line around scale cex.scale: Cex for Scale label: Logical, plot label or not label.xpos: x position for label, from left label.ypos: y position for label, from top cex.label: cex for axis labels label.col: Color for label, white is often useful for dark plots legend: Logical, plot legend (scale indicating values for colors) legend: Color for label, white is often useful for dark plots legend.pos: Character, position of legend relative to heatmap: 'l' for left, 'r' for right legend.ticks: Number of ticks to use on legend. cex.legend: cex to use for legend marks refline: Logical, Draw dashed line at coords = 0 label: Logical, plot label or not label.xpos: x position for label, from left label.ypos: y position for label, from top cex.label: cex for axis labels label.col: Color for label, white is often useful for dark plots legend: Logical, plot legend (scale indicating values for colors) legend: Color for label, white is often useful for dark plots legend.pos: Character, position of legend relative to heatmap: 'l' for left, 'r' for right legend.ticks: Number of ticks to use on legend. cex.legend: cex to use for legend marks refline: Logical, Draw dashed line at coords = 0 refline.width: Width of reference line transform: Function to transform values before plotting plot.mai: Length-4 numeric, margins around plot legend.mai: Length-4 numeric, margins around legend partition: Numeric, relative sizes of clusters partition.lines: Logical, plot lines delineating clusters partition.legend: Logical, plot cluster legend in HeatmapList partition.col: Character, colours to use for plotting clusters. Defaults to RColorBrewer's Set1 hook: Function called after plotting is complete.

Value

a list containing the specified options

See Also

plotHeatmap plotHeatmapList

Examples

myOptions = heatmapOptions()
myOptions$color = "Reds"
# plotHeatmap(hm, options=myOptions)

mgperry/heatmaps documentation built on May 22, 2019, 8:53 p.m.