plot_params: 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.