heatmapOptions: Generate default options for a Heatmap

Description Usage Arguments Value See Also Examples

Description

Generate default options for a Heatmap

Usage

1

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

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

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