plotClusterMolecules | R Documentation |
Plot cluster molecules
plotClusterMolecules(
data,
groups = NULL,
group.no = NULL,
title = NULL,
ylim = NULL,
order = NULL,
scale.center = FALSE,
scale.scale = FALSE,
frame = "white",
col = NULL,
bottom.mar = 5,
xlab = "Samples",
ylab = "Relative abundance"
)
data |
data matrix or data frame |
groups |
a vector of group memberships as returned by cutree |
group.no |
the group number to be plotted |
title |
a title for the graph |
ylim |
a vector indicating the upper and lower limit for the y-axis |
order |
whether or not to order the columns of the data matrix |
scale.center |
unless NULL, each row is scaled using scale |
scale.scale |
unless NULL, each row is scaled using scale. |
frame |
the color of the frame that is drawn as the background of the plot |
col |
If NULL, all genes will be drawn in the default color (blue). If the text "random" is given, then a set of colors will be generated by |
bottom.mar |
The size of the bottom margin of the plots as sent in par(mar=c(...)) |
xlab |
a lalel of x axis (defalt: "Samples") |
ylab |
a lalel of y axis (defalt: "Relative abundance") |
a graph
Atsushi Fukushima
this function was originally from Watson M (2005) BMC Bioinformatics 7:509
library(pcaMethods)
data(golub, package = "multtest")
hc.mol1 <- cluster.molecule(golub[, 1:27], "pearson", "average")
g1 <- cutree(hc.mol1, h=0.4)
plotClusterMolecules(golub[,1:27], g1, 3)
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