module.heatmap {Pigengene}R Documentation

Plots heatmaps for modules

Description

This function takes as input a tree and an object from pigengene-class and per any module used in the tree, it plots one gene expression heatmap.

Usage

module.heatmap(c5Tree, pigengene, saveDir, testD = NULL,
  testL = NULL, pos = 0, verbose=0, doAddEigengene=TRUE, scalePngs=1, ...)

Arguments

c5Tree

A decision tree of class C50 that uses module eigengenes, or NULL. If NULL, expression plots for all modules are created.

pigengene

A object of pigengene-class, output of compute.pigengene

saveDir

Directory to save the plots

testD, testL

Optional. The matrix of (independent) test expression data and the corresponding vector of labels

pos

Number of genes to discard. Interpreted the same way as in compact.tree ad preds.at

verbose

The integer level of verbosity. 0 means silent and higher values produce more details of computation.

doAddEigengene

If TRUE, the eigengene of each module will be added to the corresponding heatmap.

scalePngs

If not 1, the size of pngs will be adjusted using this parameter. A typical value would be 7.

...

Additional arguments. Passed to pheatmap.type

Value

A list of:

call

The call that created the results

saveDir

An echo of the input argument determining where the plots are saved

See Also

Pigengene-package, make.decision.tree, compact.tree, compute.pigengene

Examples

     ## Data:
     data(aml)
     data(mds)
     data(pigengene)
     d1 <- rbind(aml,mds)
    
     ## Fiting the trees:
     trees <- make.decision.tree(pigengene=pigengene, Data=d1,
       saveDir="trees", minPerLeaf=14:15, doHeat=FALSE,verbose=3,
       toCompact=15)

     ## Plotting:
     module.heatmap(c5Tree=trees$c5Trees[["15"]], pigengene=pigengene, 
         saveDir="heatmaps", pos=0, verbose=1)
[Package Pigengene version 1.14.0 Index]