MAMA (version 2.2.1)

metaheat: Display Data as Heatmap

Description

This function displays a matrix as a heatmap. It is based on function heatmap_2 in the Heatplus package.

Usage

metaheat(x, Rowv = NA, Colv = NA, distfun = dist, hclustfun = hclust, na.rm = TRUE, do.dendro = c(TRUE, TRUE), legend = 0, legfrac = 8, col = heat.colors(12), r.cex = NULL, c.cex = NULL, ...)

Arguments

x

the numerical data matrix to be displayed

Rowv

either a dendrogram or a vector of reordering indexes for the rows, setting to NA suppresses re-ordering of rows

Colv

either a dendrogram or a vector of reordering indexes for the columns, setting to NA suppresses re-ordering of columns

distfun

function to compute the distances between rows and columns. Defaults to dist

hclustfun

function used to cluster rows and columns. Defaults to hclust

na.rm

logical indicating whther to remove NAs

do.dendro

logical vector of length two, indicating (in this order) whether to draw the row and column dendrograms

legend

integer between 1 and 4, indicating on which side of the plot the legend should be drawn: 1=bottom, 2=left, 3=above, 4=right

legfrac

fraction of the plot that is taken up by the legend; larger values correspond to smaller legends

col

the color scheme

r.cex

font size for row labels

c.cex

font size for column labels

...

extra arguments to image

Examples

lists<-list(Method1=c("Gene_A", "Gene_V","Gene_S","Gene_C","Gene_U","Gene_D","Gene_E","Gene_G","Gene_W"), 
  Method2=c("Gene_D","Gene_W","Gene_G","Gene_E","Gene_H","Gene_X"),
  Method3=c("Gene_L","Gene_K","Gene_J","Gene_M","Gene_V","Gene_T","Gene_R","Gene_U"))
A<-make.matrix(lists)
metaheat(A, legend=1, col=c(3,4))