Heat.make: Make heatmaps from a numeric matrix.

Description Usage Arguments Details Value Author(s)

View source: R/Heat.make.R

Description

This function makes a heatmap from a numeric matrix using the package "gplots". The output is an image in pdf format.

Usage

1
  Heat.make(data.clus, cols.s=NULL, filename, filedir, rownames.vect="", cex.col=0.8, clustinrows=T,clustincols=T, toPNG=FALSE)

Arguments

data.clus

Numeric matrix with the intensity values to plot.

cols.s

Vector with colors corresponding to the conditions in the heatmap with the same order as the columns in the matrix.

filename

Name of the output file.

filedir

Name of the resultsDir.

rownames.vect

Vector with the names of the genes in the heatmap. If rownames.vect="" no rownames are shown.

cex.col

Size of the column labels.

clustinrows

TRUE if we want to order rows based on hierarchical clustering average+correlation distances.

clustincols

TRUE if we want to order columns based on hierarchical clustering Ward D2 + euclidean distances.

toPNG

TRUE if we want .png output, FALSE if we want .pdf output

Details

This function uses the package gplots to make a heatmap. The algorithm used for the dendrogram above (columns) is "ward.D2" and the algorithm used for the rows (dendrogram not shown) is "average". Column names are always in the plot, and with the option rownames=TRUE you chose weather to show or not the rownames, not recommended if you have a large number of rows. options cex.col and cex.row are used in order to change the size of row and column names respectively.

Value

The plot is created in the "filedir" directory with the name "filename" in ".pdf" format.

Author(s)

Magdalena Arnal Segura <marnal@imim.es>.


machalen/QualityGraphs documentation built on Oct. 22, 2019, 8:29 p.m.