DoHeatmap.3_MSF: 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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DoHeatmap.3_MSF(mat, facsepr = NULL, colfac, dendogram = "row",
  symb = NULL, dmeth = function(x) {     cor.dist(x, abs = F) },
  hmeth = "average", cex.genes = 0.5, cexCol = 1, margins = c(5, 15),
  ColD = FALSE, main = "", scl = "row", breaks = c(seq(-2, 2, 0.1)),
  colscheme = "gray", labRow = "", ...)

Arguments

mat

a matrix with genes in the rows and samples in the columns

facsepr

a factor in the phenotype data that separates columns in the heatmap

colfac

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

dendogram

indicates if dendogram should be added to rows, columns or both

symb

a character vector that indicates gene symbols for each row

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

cexCol

is the proportion to which columns labels should be expanded in the graphic

margins

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

ColD

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

main

is the title for the heatmap

scl

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

breaks

enable color transition at specified limits

colscheme

is the schema for colors in the body of the heatmap

Examples

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DoHeatmap.3_MSF(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.