compHclust.heatmap {compHclust} | R Documentation |
Displays a heat map of X, a dendrogram of the clustering of the columns of X and a bar plot of the relative gene importance.
compHclust.heatmap(x, xhc, gi, d.title = "Cluster Dendrogram", hm.lab = TRUE, hm.lab.cex = 1, d.ht = 0.25, gi.width = 0.5, d.mar = c(0, 4, 4, 2), hm.mar = c(5, 4, 2, 2))
x |
A numeric matrix X, where interest lies in clustering its columns. |
xhc |
An object of class hclust , specifically, a hierarchical
clustering of the columns of X. |
gi |
A vector of the relative gene importance, as returned by
compHclust . |
d.title |
The title for the dendrogram. |
hm.lab |
Logical. If true, the columns of the heat map are labeled with column numbers. |
hm.lab.cex |
The magnification to be used for the column labels
relative to the current setting of cex . See axis and
par . |
d.ht |
The relative height of the plotting region for the
dendrogram. Note that the relative height of the plotting region for
the heat map is set to 1. See layout . |
gi.width |
The relative width of the plotting region for the
relative gene importance plot. Note that the relative width of the
plotting region for the heat map is set to 1. See layout . |
d.mar |
The margins of the plotting region for the dendrogram.
See par . |
hm.mar |
The margins of the plotting region for the heat map.
See par . |
Given a numeric matrix X, a hierarchical clustering of the
columns of X and a vector of the relative gene importance as returned
by compHclust
, this function displays a heat map of X
with a dendrogram above and a bar plot of the relative gene importance
to the right. The columns of X are reordered to correspond with the
leaves of the dendrogram.
This function can be fragile - depending on the dimensions of X,
some of the arguments such as the margins, heights and widths of the
plotting regions may need to be tweaked in order for the figure to
look nice. However, it provides a quick and easy way of displaying
the output of compHclust
and seeing which genes (rows)
may be most influential in the clustering of the samples (columns).
For examples of its usage, see the help file for
compHclust
.
Gen Nowak gnowak@stanford.edu and Robert Tibshirani tibs@stanford.edu
Nowak, G. and Tibshirani, R. (18 December 2007). Complementary hierarchical clustering. Biostatistics doi:10.1093/biostatistics/kxm046.