make_comparison_matrix: Compute a similarity matrix for different strata

In slw287r/yapsa: Yet Another Package for Signature Analysis

Description

Compute and plot a similarity matrix for different strata from different stratification axes together. First, compare_sets is called on in_strata_df with itself, yielding a distance matrix (a numerical data frame) dist_df of the strata. The corresponding similarity matrix 1-dif_df is then passed to corrplot.

Usage

make_comparison_matrix(
  in_strata_df,
  output_path = NULL,
  in_nrect = 5,
  in_attribute = "",
  in_palette = NULL
)

Arguments

in_strata_df	Numerical data frame of all strata to be compared.
output_path	Path to directory where the results, especially the figure produced by corrplot is going to be stored.
in_nrect	Number of clusters in the clustering procedure provided by corrplot
in_attribute	Additional string for the file name where the figure produced by corrplot is going to be stored.
in_palette	Colour palette for the matrix

Value

The comparison matrix of cosine similarities.

See Also

compare_SMCs

Examples

data(sigs)
make_comparison_matrix(
 AlexCosmicValid_sig_df,in_nrect=9,
 in_palette=colorRampPalette(c("blue","green","red"))(n=100))

slw287r/yapsa documentation built on June 7, 2020, 12:46 a.m.