R: Plots heatmap with clustering only within types.

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

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 1.14.0 Index]