plot_dist: Plot heatmap of sample distances

Description Usage Arguments Value Author(s) Examples

View source: R/plot_dist.R

Description

Plot sample distances using rlog or other counts.

Usage

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plot_dist(rld, intgroup, col_name, output = "pheatmap",
  palette = "RdYlBu", reverse_pal = FALSE, diagNA = TRUE,
  border = NA, fontsize = 10, ...)

Arguments

rld

a matrix or DESeqTransform with assay slot

intgroup

one or more column names in colData(rld) for pheatmap annotation_col

col_name

Column name in 'colData(rld)' for labels, default is sample IDs in colnames(rld)

output

pheatmap or d3heatmap

palette

a color palette name or vector of colors

reverse_pal

reverse the color palette

diagNA

set the diagonal to NA, default TRUE

border

pheatmap border color, default none

fontsize

x and yaxis font size

...

Additional options like colors passed to d3heatmap or pheatmap

Value

A pheatmap or d3heatmap

Author(s)

Chris Stubben

Examples

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plot_dist(pasilla$rlog, c("condition", "type"), na_col="white")
plot_dist(pasilla$rlog, c("condition", "type"), palette="Blues", diagNA=FALSE, reverse=TRUE)
plot_dist(pasilla$rlog, output = "d3")

HuntsmanCancerInstitute/hciR documentation built on Jan. 10, 2020, 5:52 p.m.