plot_dist: Plot the distance between all columns of a matrix

In jcalendo/coriell: Convenience Functions for Bioinformatics

Plot the distance between all columns of a matrix

Description

Create a column-vs-column heatmap of a matrix

Usage

plot_dist(x, metadata = NULL, method = "euclidean", ...)

Arguments

x	numeric matrix or data.frame that can be converted to one. Samples in columns, features in rows.
metadata	data.frame containing metadata to be used as row labels. Default NULL.
method	distance method to be used. Must be one of the distance measure to be used. This must be one of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski"
...	additional values passed to pheatmap::pheatmap()

Value

heatmap with distance values displayed in cells.

Examples

# Generate a matrix of simulated counts
counts <- simulate_counts()$table

# Create annotation metadata
df <- data.frame(
  row.names = colnames(counts), 
  Group = rep(c("Control", "Treatment"), each = 3)
  )

# Show the sample-vs-sample distances
plot_dist(counts)

# Additional arguments can be passed to the function
plot_dist(
  x = counts, 
  metadata = df, 
  main = "Sample-vs-Sample Distance", 
  color = viridisLite::rocket(n = 50),
  annotation_colors = list(Group = c("Treatment" = "firebrick2", "Control" = "grey80"))
  )

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