Description Usage Arguments Details Value Note Author(s) See Also
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 | plotOrderedColors(
order,
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,
startAt = 0,
...)
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,
...)
|
order |
A vector giving the order of the objects. Must have the same length as |
dendro |
A hierarchical clustering dendrogram such one returned by |
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. |
rowLabels |
Labels for the colorings given in |
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 |
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
|
textPositions |
optional numeric vector of the same length as the number of columns in |
addTextGuide |
logical: should guide lines be added for the text rows (if given)? |
cex.rowLabels |
Font size scale factor for the row labels. See |
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. |
... |
Other parameters to be passed on to the plotting method (such as |
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.
None.
This function replaces plotHclustColors
in package moduleColor
.
Steve Horvath SHorvath@mednet.ucla.edu and Peter Langfelder Peter.Langfelder@gmail.com
cutreeDynamic
for module detection in a dendrogram;
plotDendroAndColors
for automated plotting of dendrograms and colors in one step.
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