pheatmap.type {Pigengene} | R Documentation

## Plots heatmap with clustering only within types.

### Description

This function first performs hierarchical clustering on samples (rows of data) within each condition. Then, plots a heatmap without further clustering of rows.

### Usage

    pheatmap.type(Data, annRow, type = colnames(annRow)[1],
    doTranspose=FALSE, conditions="Auto",...)

### Arguments

`Data` | A matrix with samples on rows and features (genes) on columns.
`annRow` | A data frame with 1 column or more. Row names must be the same as row names of Data.
`type` | The column of `annRow` used for determining the condition
`doTranspose` | If `TRUE`, the matrix will be transposed for the final plot. E.g., if the genes are on the columns of `Data`, they will be shown on rows of the heatmap.
`conditions` | A character vector that determines the conditions, and their order, to be included in the heatmap. By default ("Auto"), an alphabetical order of all available conditions in annRow will be used.
`...` | Additional arguments passed to `pheatmap` function.

### Value

A list of:

`pheatmapS` | The results of pheatmap function for each condition
`pheat` | The output of final pheatmap function applied on all data
`ordering` | The ordering of the rows in the final heatmap
`annRowAll` | The row annotation used in the final heatmap

### Note

If `type` is not determined, by default the first column of `annRow` is used.

### Author(s)

Habil Zare

### See Also

`eigengenes33`

### Examples

         data(eigengenes33)
         d1 <- eigengenes33$aml
         d2 <- eigengenes33$mds
         Disease <- c(rep("AML",nrow(d1)), rep("MDS",nrow(d2)))
         Disease <- as.data.frame(Disease)
         rownames(Disease) <- c(rownames(d1), rownames(d2))
         p1 <- pheatmap.type(rbind(d1,d2),annRow=Disease,show_rownames=FALSE)

[Package Pigengene version 1.12.0 Index]