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. Alternatively, it can plot a heatmap for every module in the given `pigengene` object.

### Usage

    module.heatmap(c5Tree=NULL, pigengene, mes=NULL, 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`
`mes` | A character vector that determines which modules to plot, e.g., c("ME3","ME5"). Set it to `NULL` to plot a heatmap for every module. This argument will be ignored if `c5Tree` is not `NULL`.
`saveDir` | Directory to save the plots
`testD, testL` | Optional. The matrix of (independent) test expression data, and the corresponding vector of labels. `testL` must be named according to the row names of `testD`.
`pos` | Number of genes to discard. Interpreted the same way as in `compact.tree` and `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)

         ## 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)

[Package Pigengene version 1.16.0 Index]