Usage
plotClusterTreeSamples(
datExpr,
y = NULL,
traitLabels = NULL,
yLabels = NULL,
main = if (is.null(y)) "Sample dendrogram" else "Sample dendrogram and trait indicator",
setLayout = TRUE, autoColorHeight = TRUE, colorHeight = 0.3,
dendroLabels = NULL,
addGuide = FALSE, guideAll = TRUE,
guideCount = NULL, guideHang = 0.2,
cex.traitLabels = 0.8,
cex.dendroLabels = 0.9,
marAll = c(1, 5, 3, 1),
saveMar = TRUE,
abHeight = NULL, abCol = "red",
...)
Arguments
datExpr
a data frame containing expression data, with rows corresponding to samples and
columns to genes. Missing values are allowed and will be ignored.
y
microarray sample trait. Either a vector with one entry per sample, or a matrix in which each
column corresponds to a (different) trait and each row to a sample.
traitLabels
labels to be printed next to the color rows depicting sample traits. Defaults to
column names of y.
yLabels
Optional labels to identify colors in the row identifying the sample classes.
If given, must be of the same dimensions as y. Each label that occurs will be displayed
once.
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.
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.
cex.traitLabels
character expansion factor for trait labels.
cex.dendroLabels
character expansion factor for dendrogram (sample) labels.
marAll
a 4-element vector giving the bottom, left, top and right margins around the combined
plot. Note that this is not the same as setting the margins via a call to par, because the
bottom margin of the dendrogram 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.