doClusterTableFCH_fromMatrix: A function that creates a heatmap with column indicators on...
In mssm-msf-2019/BiostatsALL:

Description Usage Arguments Examples

This function creates a nice heatmap for publication. It puts on top of each column a color indicator of what sample type it is, does clustering, and adds a table in the right margin of the figure with logFoldChanges and respective significance indicators (stars).

doClusterTableFCH_fromMatrix(mat, ps = rownames(mat), colfac,
  facsepr = NULL, hmeth = "average", dmeth = cor.dist, coefs, fdrs,
  main = "", ColD = FALSE, ss = ps, gn = NULL, breaks = NULL,
  cexg = 1, margins = c(5, 20))

`mat`	numeric matrix to cluster. Usually th raw expression data.
`facsepr`	factor to separate columns in the heatmaps
`hmeth`	aglomeration strategy
`dmeth`	aglomeration distance to cluster
`coefs`	estimates to be drawn tin the tabl (eg lgFCHs)
`fdrs`	p values or fdr indicating significance of the estimates; should be the same dim as coefs
`ColD`	logical TRUE if cluster by rows and columns
`gn`	gene name
`colfc`	factor to add colored legend to the heatmap
`sn`	edited names for the rows (if different than the rownames) eg symbols for probesets

1	doClusterTableFCH_fromMatrix(mat,ps=rownames(mat),colfac,facsepr=NULL,hmeth='average',dmeth=cor.dist,coefs,fdrs,main="", ColD=FALSE, ss=ps, gn=NULL, breaks=NULL,cexg=1,margins=c(5,20) )