In vladpetyuk/vp.misc: Miscellaneous functions used by Vlad Petyuk for proteomics data analysis

library("vp.misc")
suppressPackageStartupMessages(library("MSnbase"))

data(srm_msnset)

# match.group, subject.type, msex, Visible blood contamination
columnCol <- pData(msnset)[,c("subject.type", "match.group", "msex", 
                              "Visible blood contamination")]
columnCol <- as.data.frame(lapply(columnCol, as.factor))
columnCol$subject.type <- 
    c('red','orange','blue')[columnCol$subject.type]
columnCol$match.group <- 
    jet.colors(nlevels(columnCol$match.group))[columnCol$match.group]
columnCol$msex <- 
    c('pink','olivedrab')[columnCol$msex]
columnCol$Visible.blood.contamination <- 
    c('black','lightgrey')[columnCol$Visible.blood.contamination]

heatmap.plus.2(exprs(msnset), 
               hclustfun = function(x, ...) hclust(x, method="ward.D", ...),
               dist = function(x, ...) dist(x, method="pearson", ...),
               propColSide=0.1,
               scale="none",
               ColSideColors=as.matrix(columnCol),
               breaks=c(-4,seq(-2,+2,length=100),+4),
               col=gplots::bluered(102-1)
               )

vladpetyuk/vp.misc documentation built on June 25, 2021, 6:35 a.m.