WGCNA: plotColorUnderTree – R documentation

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plotColorUnderTree

Plot color rows in a given order, for example under a dendrogram

Description

Plot color rows encoding information about objects in a given order, for example the order of a clustering dendrogram, usually below the dendrogram or a barplot.

Usage

plotOrderedColors(
   order, 
   colors, 
   main = "",
   rowLabels = NULL, 
   rowWidths = NULL, 
   rowText = NULL,
   rowTextAlignment = c("left", "center", "right"),
   rowTextIgnore = NULL,
   textPositions = NULL, 
   addTextGuide = TRUE,
   cex.rowLabels = 1, 
   cex.rowText = 0.8,
   startAt = 0,
   align = c("center", "edge"),
   separatorLine.col = "black",
   ...)

plotColorUnderTree(
   dendro, 
   colors,
   rowLabels = NULL,
   rowWidths = NULL,
   rowText = NULL,
   rowTextAlignment = c("left", "center", "right"),
   rowTextIgnore = NULL,
   textPositions = NULL,
   addTextGuide = TRUE,
   cex.rowLabels = 1,
   cex.rowText = 0.8,
   separatorLine.col = "black",
   ...)

Arguments

`order`	A vector giving the order of the objects. Must have the same length as `colors` if `colors` is a vector, or as the number of rows if `colors` is a matrix or data frame.
`dendro`	A hierarchical clustering dendrogram such one returned by `hclust`.
`colors`	Coloring of objects on the dendrogram. Either a vector (one color per object) or a matrix (can also be an array or a data frame) with each column giving one color per object. Each column will be plotted as a horizontal row of colors under the dendrogram.
`main`	Optional main title.
`rowLabels`	Labels for the colorings given in `colors`. The labels will be printed to the left of the color rows in the plot. If the argument is given, it must be a vector of length equal to the number of columns in `colors`. If not given, `names(colors)` will be used if available. If not, sequential numbers starting from 1 will be used.
`rowWidths`	Optional specification of relative row widths for the color and text (if given) rows. Need not sum to 1.
`rowText`	Optional labels to identify colors in the color rows. If given, must be of the same dimensions as `colors`. Each label that occurs will be displayed once.
`rowTextAlignment`	Character string specifying whether the labels should be left-justified to the start of the largest block of each label, centered in the middle, or right-justified to the end of the largest block.
`rowTextIgnore`	Optional specifications of labels that should be ignored when displaying them using `rowText` above.
`textPositions`	optional numeric vector of the same length as the number of columns in `rowText` giving the color rows under which the text rows should appear.
`addTextGuide`	logical: should guide lines be added for the text rows (if given)?
`cex.rowLabels`	Font size scale factor for the row labels. See `par`.
`cex.rowText`	character expansion factor for text rows (if given).
`startAt`	A numeric value indicating where in relationship to the left edge of the plot the center of the first rectangle should be. Useful values are 0 if ploting color under a dendrogram, and 0.5 if ploting colors under a barplot.
`align`	Controls the alignment of the color rectangles. `"center"` means aligning centers of the rectangles on equally spaced values; code"edge" means aligning edges of the first and last rectangles on the edges of the plot region.
`separatorLine.col`	Color of the line separating rows of color rectangles. If `NA`, no lines will be drawn.
`...`	Other parameters to be passed on to the plotting method (such as `main` for the main title etc).

Details

It is often useful to plot dendrograms or other plots (e.g., barplots) of objects together with additional information about the objects, for example module assignment (by color) that was obtained by cutting a hierarchical dendrogram or external color-coded measures such as gene significance. This function provides a way to do so. The calling code should section the screen into two (or more) parts, plot the dendrogram (via plot(hclust)) or other information in the upper section and use this function to plot color annotation in the order corresponding to the dendrogram in the lower section.

Value

A list with the following components

colorRectangles

A list with one component per color row. Each component is a list with 4 elements xl, yb, xr, yt giving the left, bottom, right and top coordinates of the rectangles in that row.

Note

This function replaces plotHclustColors in package moduleColor.

Author(s)

Steve Horvath SHorvath@mednet.ucla.edu and Peter Langfelder Peter.Langfelder@gmail.com