heatmap.3: Heatmap

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

Description

Customized Heatmap. TO FILL WHAT EXACTLY IS CUSTOM ABOUT IT.

Usage

heatmap.3(
  x,
  dist.fun = c("euclidean", "pearson"),
  na.avg = TRUE,
  col.ramp = bluered,
  z.transf = c(FALSE, TRUE),
  breaks = seq(-1, +1, length = 100),
  linkage = c("average", "ward.D", "ward.D2", "single", "complete", "mcquitty",
    "median", "centroid"),
  nLabLim = 30,
  ...
)

Arguments

x	MSnSet object
dist.fun	distance function "euclidean" or"pearson"
na.avg	logical. Should NA distances be assigned just an average value?
col.ramp	color mapping function. default gplots::bluered
z.transf	logical perform Z-transform or not.
breaks	color key breaks
linkage	see ?hclust
nLabLim	max limit of the row/column labels to show. default 30
...	further arguments to gplots::heatmap.2

Examples

data(srm_msnset)
set.seed(0)
clrz <- sample(colors(), 17)
heatmap.3(cor(exprs(msnset)), 
          dist.fun="pearson",
          linkage="average", 
          nLabLim=50,
          ColSideColors=c('red3','yellow3','green3')[as.factor(pData(msnset)$subject.type)],
          RowSideColors=clrz[as.factor(pData(msnset)$match.group)])

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