WGCNA: plotDendroAndColors – R documentation

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plotDendroAndColors

Dendrogram plot with color annotation of objects

Description

This function plots a hierarchical clustering dendrogram and color annotation(s) of objects in the dendrogram underneath.

Usage

plotDendroAndColors(
  dendro, 
  colors, 
  groupLabels = NULL, 
  rowText = NULL,
  rowTextAlignment = c("left", "center", "right"),
  rowTextIgnore = NULL,
  textPositions = NULL,
  setLayout = TRUE, 
  autoColorHeight = TRUE, 
  colorHeight = 0.2, 
  colorHeightBase = 0.2, 
  colorHeightMax = 0.6,
  rowWidths = NULL, 
  dendroLabels = NULL, 
  addGuide = FALSE, guideAll = FALSE, 
  guideCount = 50, guideHang = 0.2, 
  addTextGuide = FALSE,
  cex.colorLabels = 0.8, cex.dendroLabels = 0.9, 
  cex.rowText = 0.8,
  marAll = c(1, 5, 3, 1), saveMar = TRUE, 
  abHeight = NULL, abCol = "red", ...)

Arguments

`dendro`	a hierarchical clustering dendrogram such as one produced 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.
`groupLabels`	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.
`rowText`	Optional labels to identify colors in the color rows. If given, must be either the same dimensions as `colors` or must have the same number of rows and `textPositions` must be used to specify which columns of `colors` each column of `rowText` corresponds to. Each label that occurs will be displayed once, under the largest continuous block of the corresponding `colors`.
`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.
`setLayout`	logical: should the plotting device be partitioned into a standard layout? If `FALSE`, the user is responsible for partitioning. The function expects two regions of the same width, the first one immediately above the second one.
`autoColorHeight`	logical: should the height of the color area below the dendrogram be automatically adjusted for the number of traits? Only effective if `setLayout` is `TRUE`.
`colorHeight`	specifies the height of the color area under dendrogram as a fraction of the height of the dendrogram area. Only effective when `autoColorHeight` above is `FALSE`.
`colorHeightBase`	when `autoColorHeight` is `TRUE`, this specifies the minimum height of the color area (the height when there is one color row).
`colorHeightMax`	when `autoColorHeight` is `TRUE`, this specifies the maximum height of the color area (the height when there are many color rows).
`rowWidths`	optional specification of relative row widths for the color and text (if given) rows. Need not sum to 1.
`dendroLabels`	dendrogram labels. Set to `FALSE` to disable dendrogram labels altogether; set to `NULL` to use row labels of `datExpr`.
`addGuide`	logical: should vertical "guide lines" be added to the dendrogram plot? The lines make it easier to identify color codes with individual samples.
`guideAll`	logical: add a guide line for every sample? Only effective for `addGuide` set `TRUE`.
`guideCount`	number of guide lines to be plotted. Only effective when `addGuide` is `TRUE` and `guideAll` is `FALSE`.
`guideHang`	fraction of the dendrogram height to leave between the top end of the guide line and the dendrogram merge height. If the guide lines overlap with dendrogram labels, increase `guideHang` to leave more space for the labels.
`addTextGuide`	logical: should guide lines be added for the text rows (if given)?
`cex.colorLabels`	character expansion factor for trait labels.
`cex.dendroLabels`	character expansion factor for dendrogram (sample) labels.
`cex.rowText`	character expansion factor for text rows (if given).
`marAll`	a vector of length 4 giving the bottom, left, top and right margins of the combined plot. There is no margin between the dendrogram and the color plot underneath.
`saveMar`	logical: save margins setting before starting the plot and restore on exit?
`abHeight`	optional specification of the height for a horizontal line in the dendrogram, see `abline`.
`abCol`	color for plotting the horizontal line.
`...`	other graphical parameters to `plot.hclust`.

Details

The function slits the plotting device into two regions, plots the given dendrogram in the upper region, then plots color rows in the region below the dendrogram.

Value

None.

Author(s)

Peter Langfelder