module.heatmap {Pigengene} | R Documentation |
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. Alternatively, it can plot
a heatmap for every module in the given pigengene
object.
module.heatmap(c5Tree=NULL, pigengene, mes=NULL, saveDir, testD = NULL, testL = NULL, pos = 0, verbose=0, doAddEigengene=TRUE, scalePngs=1, ...)
c5Tree |
A decision tree of class |
pigengene |
A object of |
mes |
A character vector that determines which modules to plot, e.g.,
c("ME3","ME5"). Set it to |
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
|
verbose |
The integer level of verbosity. 0 means silent and higher values produce more details of computation. |
doAddEigengene |
If |
scalePngs |
If not 1, the size of pngs will be adjusted using this parameter. A typical value would be 7. |
... |
Additional arguments. Passed to |
A list of:
call |
The call that created the results |
saveDir |
An echo of the input argument determining where the plots are saved |
Pigengene-package
,
make.decision.tree
, compact.tree
,
compute.pigengene
## Data: data(aml) data(mds) data(pigengene) d1 <- rbind(aml,mds) ## Plotting the heatmaps of all modules: module.heatmap(pigengene=pigengene, saveDir="heatmaps", pos=0, verbose=1) ## Fiting the trees: trees <- make.decision.tree(pigengene=pigengene, Data=d1, saveDir="trees", minPerLeaf=14:15, doHeat=FALSE,verbose=3, toCompact=15) ## Plotting the heatmaps of only the modules in the tree: module.heatmap(c5Tree=trees$c5Trees[["15"]], pigengene=pigengene, saveDir="treeHeatmaps", pos=0, verbose=1)