Usage
plotSquareHeatmap(values, palette, vlim, mas, na.indices.x = NULL, na.indices.y = NULL, na.col = "#bdbdbd", xaxt = NULL, yaxt = NULL, plotModuleNames = TRUE, main = "", main.line = 0, plotLegend = TRUE, legend.main = "", legend.main.line = 1, xaxt.line = -0.5, yaxt.line = -0.5, maxt.line = 3, laxt.tck = 0.04, laxt.line = 2.5, legend.line = 0.1, lwd = 2, dryRun = FALSE)
Arguments
values
values to plot on the heatmap.
palette
color palette to interpolate over.
vlim
range of values to use when mapping values to the palette.
mas
ordered subset of the moduleAssignments vector.
na.indices.x
indices of missing values on the x axis.
na.indices.y
indices of missing values on the y axis.
na.col
color of missing values to plot.
xaxt
character vector of names to print along the x axis.
yaxt
character vector of names to print along the y axis.
plotModuleNames
logical; if TRUE the names of the modules are
plotted along the x axis if values is not symmetric, and along both
axes if values is symettric.
main.line
the number of lines into the top margin at which the plot
title will be drawn.
plotLegend
logical; if TRUE a legend is added to the right
side of the plot.
legend.main
title for the legend.
legend.main.line
distance from the legend to render the legend
title.
xaxt.line
the number of lines into the margin at which the x axis
labels will be drawn.
yaxt.line
the number of lines into the margin at which the y axis
labels will be drawn.
maxt.line
the number of lines into the margin at which the module
names will be drawn.
laxt.tck
size of the ticks on the axis legend as a proportion
of the horizontal size of the plot window.
laxt.line
the distance from the legend to render the legend axis
labels, as multiple of laxt.tck.
legend.line
the distance from the plot to render the legend as a
proportion of the horizontal size of the plot window.
lwd
line width for borders.
dryRun
logical; if TRUE only the axes and borders will be
drawn.