quickmap: Heatmap with sensible defaults for RNA-seq expression data

In jcalendo/coriell: Convenience Functions for Bioinformatics

Heatmap with sensible defaults for RNA-seq expression data

Description

Generate a heatmap using pheatmap with sensible defaults for RNA-seq.

Usage

quickmap(x, metadata = NULL, remove_var = NULL, ...)

Arguments

x	numeric matrix to be passed onto pheatmap function
metadata	column metadata to add to heatmap annotation. Default NULL
remove_var	Remove this proportion of features based on variance across rows. Default NULL.
...	args to be passed to pheatmap() function

Details

The default arguments to pheatmap::pheatmap() are:

• scale = "row"

• show_rownames = FALSE

• border_col = NA

• cluster_rows = TRUE

• cluster_cols = TRUE

• color = colorRampPalette(c("dodgerblue3", "grey99", "firebrick3"))(30)

• treeheight_row = 0

• clustering_distance_rows = "correlation"

• clustering_distance_cols = "euclidean"

• clustering_method = "ward.D2"

• angle_col = 315

Value

pheatmap object. See ?pheatmap::pheatmap() for details

Examples

# Display heatmap of scaled count data and add title to the plot
quickmap(GSE161650_lc, main = "THZ1 vs DMSO")

# Override quickmap defaults by supplying additional args
quickmap(GSE161650_lc, cluster_rows = FALSE, cluster_cols = FALSE)

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.