Usage
plotDendroAndColors(
dendro,
colors,
groupLabels = NULL,
rowText = NULL,
rowTextAlignment = c("left", "center", "right"),
rowTextIgnore = NULL,
textPositions = NULL,
setLayout = TRUE,
autoColorHeight = TRUE,
colorHeight = 0.2,
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 dendrogra
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,
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 e
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.
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.