plot_params: Template parameters

Description Arguments

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.


NetRep documentation built on June 12, 2018, 5:04 p.m.