DiffCorr (version 0.4.4)

plotClusterMolecules: Plot cluster molecules

Description

Plot cluster molecules

Usage

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"
)

Value

a graph

Arguments

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")

Author

Atsushi Fukushima

References

this function was originally from Watson M (2005) BMC Bioinformatics 7:509

Examples

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)