DoHeatmapSamples: A function that draws a heatmap based on a matrix

Description Usage Arguments Examples

Description

a function that is supposed to draw a heatmap based on a matrix of gene expressions

Usage

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DoHeatmapSamples(exprs, corm = "pearson", colfac = NULL, dmeth = euc,
  hmeth = "average", cex.genes = 0.5, margins = c(5, 15), main = "",
  scl = "none", thebreaks = NULL, samplelabels = NULL, colcol = NULL,
  ...)

Arguments

exprs

is a matrix of expressions

corm

is the metric for correlation evaluation

colfac

a factor in the phenotype data that will add colors to the top according to different levels

dmeth

the method to measure distance between matrices rows

hmeth

the method for the hierarchical clustering

cex.genes

is the proportion to which genes symbols should be expanded in the graphic

margins

is the definition of vertical and horizontal margins to plot the heatmap

main

is the title for the heatmap

scl

is an indicator if data should be scaled by row, column or both

thebreaks

enable color transition at specified limits

samplelabels

keeps a vector of characters to be used in the heatmap columns

colcol

is the color schema for the rows

ColD

is a logical parameter that indicates if the columns should be clustered

colscheme

is the schema for colors in the body of the heatmap

Examples

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DoHeatmap(mat = exprs(eset),facsepr = mygroup1, colfac = mygroup2, symb = genesymbols, dmeth=cor.dist, hmeth='average',
cex.genes=0.5, margins = c(5,15), main='', scl = row, breaks = NULL, cexCol = 1, colscheme = 'gray')

mssm-msf-2019/BiostatsALL documentation built on May 22, 2019, 12:16 p.m.