plotDendroAndColors {WGCNA}

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

See Also

plotColorUnderTree