plot_params: Template parameters

In InouyeLab/NetRep: Permutation Testing Network Module Preservation Across Datasets

Description

Template parameters to be imported into other function documentation. This is not intended to be a stand-alone help file.

Arguments

orderNodesBy	NULL (default), NA, or a vector of dataset names or indices. Controls how nodes are ordered on the plot (see details).
orderSamplesBy	NULL (default), NA, or a vector containing a single dataset name or index. Controls how samples are ordered on the plot (see details).
plotNodeNames	logical; controls whether the node names are drawed on the bottom axis.
plotSampleNames	logical; controls whether the sample names are drawed on the left axis.
plotModuleNames	logical; controls whether module names are drawed. The default is for module names to be drawed when multiple modules are drawn.
main	title for the plot.
main.line	the number of lines into the top margin at which the plot title will be drawn.
drawBorders	logical; if TRUE, borders are drawn around the weighted degree, node conribution, and module summary bar plots.
lwd	line width for borders and axes.
naxt.line	the number of lines into the bottom margin at which the node names will be drawn.
saxt.line	the number of lines into the left margin at which the sample names will be drawn.
maxt.line	the number of lines into the bottom margin at which the module names will be drawn.
xaxt.line	the number of lines into the bottom margin at which the x-axis tick labels will be drawn on the module summary bar plot.
xaxt.tck	the size of the x-axis ticks for the module summary bar plot.
xlab.line	the number of lines into the bottom margin at which the x axis label on the module summary bar plot(s) will be drawn.
yaxt.line	the number of lines into the left margin at which the y-axis tick labels will be drawn on the weighted degree and node contribution bar plots.
ylab.line	the number of lines into the left margin at which the y axis labels on the weighted degree and node contribution bar plots will be drawn.
yaxt.tck	the size of the y-axis ticks for the weighted degree and node contribution bar plots.
laxt.line	the distance from the legend to draw the legend axis labels, as multiple of laxt.tck.
laxt.tck	size of the ticks on each axis legend relative to the size of the correlation, edge weights, and data matrix heatmaps.
legend.main.line	the distance from the legend to draw the legend title.
cex.axis	relative size of the node and sample names.
cex.lab	relative size of the module names and legend titles.
cex.main	relative size of the plot titles.
dataCols	a character vector of colors to create a gradient from for the data heatmap (see details). Automatically determined if NA or NULL.
dataRange	the range of values to map to the dataCols gradient (see details). Automatically determined if NA or NULL.
corCols	a character vector of colors to create a gradient from for the correlation structure heatmap (see details).
corRange	the range of values to map to the corCols gradient (see details).
netCols	a character vector of colors to create a gradient from for the network edge weight heatmap (see details).
netRange	the range of values to map to the corCols gradient (see details). Automatically determined if NA or NULL.
degreeCol	color to use for the weighted degree bar plot.
contribCols	color(s) to use for the node contribution bar plot (see details).
summaryCols	color(s) to use for the node contribution bar plot (see details).
naCol	color to use for missing nodes and samples on the data, correlation structure, and network edge weight heat maps.
dryRun	logical; if TRUE, only the axes and labels will be drawed.

InouyeLab/NetRep documentation built on Oct. 8, 2020, 2:32 a.m.