plot_correlation_matrix: Draw correlation matrix of radiomic features

In cgplab/RadAR: Radiomic Analysis with R

Description

This function draws a correlation matrix of the radiomic dataset by corrplot or pheatmap. Correlation matrix can be visualized by clustered correlation plot or heatmap.

Usage

plot_correlation_matrix(
  rdr = NULL,
  view_as = c("heatmap", "corrplot"),
  method_correlation = "pearson",
  method_hcl = "ward.D",
  which_data = "normal",
  cex_labels = 0.5,
  srt_labels = 45,
  ncolors = 50,
  save_plot_to = NULL,
  width_plot = 20,
  height_plot = 15,
  show_names = T,
  show_dendrogram = T
)

Arguments

rdr	A RadAR object (class SummarizedExperiment).
view_as	(character) How to visualize correlation matrix? It can be "corrplot" or "heatmap".
method_correlation	(character) Which method use to calculate correlation. It can be one of the following: "pearson", "kendall", "spearman".
method_hcl	(character) Which method use for clustering matrix columns and rows. Available methods are "ward.D", "ward.D2", "single", "complete","average" , "mcquitty","median", "centroid".
which_data	(character) Which data use for the computation of the correlation coefficients. It can be one of the following: "normal", "scaled", "normalized".
cex_labels	(numeric) Text label cex.
srt_labels	(numeric) Text label string rotation in degrees.
ncolors	(numeric) Number of colors to generate the palette.
save_plot_to	(character) If specified, filename where the heatmap will be saved to.
width_plot	(numeric) output file width in inches.
height_plot	(numeric) output file height in inches.
show_names	(logical) Should feature names (labels) be visualized?
show_dendrogram	(logical) Should dendogram (for columns and rows) be drawn (valid for heatmap visualzation)?

Value

none

Author(s)

Matteo Benelli ([e-mail])

cgplab/RadAR documentation built on Nov. 10, 2021, 1:32 a.m.