Description Usage Arguments Examples
a function that is supposed to draw a heatmap based on a matrix of gene expressions
1 2 3 4 5 |
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 |
1 2 | 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')
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