WGCNA: labeledHeatmap.multiPage – R documentation

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labeledHeatmap.multiPage

Labeled heatmap divided into several separate plots.

Description

This function produces labaled heatmaps divided into several plots. This is useful for large heatmaps where labels on individual columns and rows may become unreadably small (or overlap).

Usage

labeledHeatmap.multiPage(
   # Input data and ornaments
   Matrix, 
   xLabels, yLabels = NULL,
   xSymbols = NULL, ySymbols = NULL,
   textMatrix = NULL, 

   # Paging options
   rowsPerPage = NULL, maxRowsPerPage = 20, 
   colsPerPage = NULL, maxColsPerPage = 10, 
   addPageNumberToMain = TRUE, 

   # Further arguments to labeledHeatmap
   zlim = NULL,
   signed = TRUE, 
   main = "", 
   ...)

Arguments

`Matrix`	numerical matrix to be plotted in the heatmap.
`xLabels`	labels for the columns. See Details.
`yLabels`	labels for the rows. See Details.
`xSymbols`	additional labels used when `xLabels` are interpreted as colors. See Details.
`ySymbols`	additional labels used when `yLabels` are interpreted as colors. See Details.
`textMatrix`	optional text entries for each cell. Either a matrix of the same dimensions as `Matrix` or a vector of the same length as the number of entries in `Matrix`.
`rowsPerPage`	optional list in which each component is a vector specifying which rows should appear together in each plot. If not given, will be generated automatically based on `maxRowsPerPage` below and the number of rows in `Matrix`.
`maxRowsPerPage`	integer giving maximum number of rows appearing on each plot (page).
`colsPerPage`	optional list in which each component is a vector specifying which columns should appear together in each plot. If not given, will be generated automatically based on `maxColsPerPage` below and the number of rows in `Matrix`.
`maxColsPerPage`	integer giving maximum number of columns appearing on each plot (page).
`addPageNumberToMain`	logical: should plot/page number be added to the `main` title of each plot?
`zlim`	Optional specification of the extreme values for the color scale. If not given, will be determined from the input `Matrix`.
`signed`	logical: should the input `Matrix` be converted to colors using a scale centered at zero?
`main`	Main title for each plot/page, optionally with the plot/page number added.
`...`	other arguments to function `labeledHeatmap`.

Details

The function labeledHeatmap is used to produce each plot/page; most arguments are described in more detail in the help file for that function.

In each plot/page labeledHeatmap plots a standard heatmap plot of an appropriate sub-rectangle of Matrix and embellishes it with row and column labels and/or with text within the heatmap entries. Row and column labels can be either character strings or color squares, or both.

To get simple text labels, use colorLabels=FALSE and pass the desired row and column labels in yLabels and xLabels, respectively.

To label rows and columns by color squares, use colorLabels=TRUE; yLabels and xLabels are then expected to represent valid colors. For reasons of compatibility with other functions, each entry in yLabels and xLabels is expected to consist of a color designation preceded by 2 characters: an example would be MEturquoise. The first two characters can be arbitrary, they are stripped. Any labels that do not represent valid colors will be considered text labels and printed in full, allowing the user to mix text and color labels.

It is also possible to label rows and columns by both color squares and additional text annotation. To achieve this, use the above technique to get color labels and, additionally, pass the desired text annotation in the xSymbols and ySymbols arguments.

If rowsPerPage (colsPerPage) is not given, rows (columns) are allocated automatically as uniformly as possible, in contiguous blocks of size at most maxRowsPerPage (maxColsPerPage). The allocation is performed by the function allocateJobs.

Value

None.

Author(s)

Peter Langfelder