iheatmap-SummarizedExperiment: Summarized Experiment iheatmap and iheatmap methods
In skummerf/GenomicWidgets: interactive visualization of genomics data

Description Usage Arguments Value Examples

iheatmap methods that take as input a SummarizedExperiment object. With SummarizedExperiment input, the defaults are different than with a plain matrix input, and more likely to be suitable for functional genomics data.

## S4 method for signature 'SummarizedExperiment'
iheatmap(data, assay = assayNames(data)[[1]],
  x = se_default_x(data, assay), y = se_default_y(data, assay),
  cluster_rows = c("hclust", "kmeans", "none"), cluster_cols = c("hclust",
  "kmeans", "none"), scale = "rows", ...)

## S4 method for signature 'IheatmapHorizontal,SummarizedExperiment'
add_iheatmap(p, data,
  assay = assayNames(data)[[1]], x = se_default_x(data),
  cluster_cols = c("hclust", "kmeans", "none"), scale = "rows", ...)

## S4 method for signature 'IheatmapVertical,SummarizedExperiment'
add_iheatmap(p, data,
  assay = assayNames(data)[[1]], y = se_default_y(data),
  cluster_rows = c("hclust", "kmeans", "none"), scale = "rows", ...)

`data`	SummarizedExperiment
`assay`	name of assay in data to plot
`x`	name of rows of data, by default rownames
`y`	name of columns of data, by default colnames
`cluster_rows`	how to cluster rows, default is hclust
`cluster_cols`	how to cluster columns, default is hclust
`scale`	scale rows, columns, both, or none
`...`	additional arguments to `iheatmap`
`p`	IHeatmap object

Iheatmap-class object

library(SummarizedExperiment)
data(rpkm_chr21)

hm <- iheatmap(rpkm_chr21, "rpkm",
               x = colData(rpkm_chr21)$STD_NAME, 
               y = rowData(rpkm_chr21)$SYMBOL, 
               col_annotation = colData(rpkm_chr21)[,c("TYPE","SEX")])
               
if (interactive()) {
  hm
}