Plot correlation matrix — plot_cor

Plot correlation matrix between samples as a heatmap

Usage

plot_cor_matrix(
  se_obj,
  use = "pairwise.complete.obs",
  method = c("spearman", "pearson", "kendall"),
  label_group = TRUE,
  label_time = TRUE,
  label_rep = TRUE,
  label_batch = TRUE,
  show_rownames = FALSE,
  show_colnames = FALSE,
  fontsize = 8,
  cellwidth = 1,
  cellheight = 1,
  title = "Correlation between samples",
  ...
)

Arguments

se_obj: A SummarizedExperiment object created by check_input()
use: Parameter of stats::cor() (default is "pairwise.complete.obs")
method: Parameter of stats::cor() (default is "spearman")
label_group: Whether to label Group (default is TRUE)
label_time: Whether to label Time (default is TRUE)
label_rep: Whether to label Replicate (default is TRUE)
label_batch: Whether to label Batch (default is TRUE)
show_rownames: Whether to show row names in the heatmap (default is FALSE)
show_colnames: Whether to show column names in the heatmap (default is FALSE)
fontsize: Font size for the heatmap and annotations (default is 8)
cellwidth: Cell width for the heatmap (default is 1)
cellheight: Cell height for the heatmap (default is 1)
title: Title of the heatmap (default is "Correlation between samples")
...: Additional arguments to be passed to ComplexHeatmap::Heatmap()

Value

A heatmap showing the correlation between samples.

Examples

data("example")
plot_cor_matrix(example_obj)