plot_params: Template parameters
In NetRep: Permutation Testing Network Module Preservation Across Datasets

plot_params

R Documentation

Template parameters

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.