plot_cor_pairs: Plot pairwise correlations between columns of a matrix

In jcalendo/coriell: Convenience Functions for Bioinformatics

Plot pairwise correlations between columns of a matrix

Description

Plot the pairwise correlations between pairs of samples in a matrix. Histograms, correlation values, and smooth scatters with loess fits are visualized in each panel. Inspired by 'methylKit::getCorrelation(..., plot=TRUE)' and examples in 'pairs()'

Usage

plot_cor_pairs(
  m,
  hist_breaks = 30,
  hist_col = "grey50",
  cor_method = c("pearson", "kendall", "spearman"),
  cor_use = "everything",
  cor_digits = 2,
  cor_cex = 2,
  scatter_colramp = hcl.colors,
  scatter_ab_col = "red2",
  scatter_ab_lty = 2,
  scatter_ab_lwd = 1,
  scatter_crv_col = "red3",
  scatter_crv_lwd = 2,
  scatter_crv_lty = 1,
  cex_labels = 2,
  font_labels = 1
)

Arguments

m	Matrix with features in rows and Samples in columns
hist_breaks	Number of breaks to use in histogram
hist_col	Color of the histogram bars
cor_method	Method to use for calculating correlations. One of "pearson" (default), "kendall", or "spearman": can be abbreviated
cor_use	an optional character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything", "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs".
cor_digits	Number of digits to report in correlations
cor_cex	Character expansion size for correlation values
scatter_colramp	function accepting an integer n as an argument and returning n colors used in the smoothScatter plots
scatter_ab_col	Color of the abline of the smoothScatter plots
scatter_ab_lty	Line type of the abline of the smoothScatter plots
scatter_ab_lwd	Line weight of the abline of the smoothScatter plots
scatter_crv_col	Color of the lowess lines of the smoothScatter plots
scatter_crv_lwd	Line weight of the lowess lines of the smoothScatter plots
scatter_crv_lty	Line type of the lowess lines of the smoothScatter plots
cex_labels	Text panel graphics parameters passed to 'pairs()'
font_labels	Text panel graphics parameters passed to 'pairs()'

Value

pairs plot

Examples

plot_cor_pairs(GSE161650_lc)

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