pheatmap.type {Pigengene} | R Documentation |
This function first performs hierarchical clustering on samples (rows of data) within each condition. Then, plots a heatmap without further clustering of rows.
pheatmap.type(Data, annRow, type = colnames(annRow)[1], doTranspose=FALSE, conditions="Auto",...)
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 |
doTranspose |
If |
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 |
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 |
If type
is not determined, by default the first column of
annRow
is used.
Habil Zare
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(Data=rbind(d1,d2),annRow=Disease,show_rownames=FALSE)