sigminer (version 0.1.11)

draw_sig_corrplot: Plot correlation between signature activities

Description

Plot correlation between signature activities

Usage

draw_sig_corrplot(mat_list, order = "original", type = "lower",
  sig.level = 0.05, ...)

Arguments

mat_list

a list contain correlation and p value matrix etc., obtain it from sig_get_correlation function.

order

Character, the ordering method of the correlation matrix.

• "original" for original order (default).

• "AOE" for the angular order of the eigenvectors.

• "FPC" for the first principal component order.

• "hclust" for the hierarchical clustering order.

• "alphabet" for alphabetical order.

See function corrMatOrder for details.

type

Character, "full" (default), "upper" or "lower", display full matrix, lower triangular or upper triangular matrix.

sig.level

Significant level, if the p-value in p-mat is bigger than sig.level, then the corresponding correlation coefficient is regarded as insignificant. If insig is "label_sig", this may be an increasing vector of significance levels, in which case pch will be used once for the highest p-value interval and multiple times (e.g. "*", "**", "***") for each lower p-value interval.

...

other arguments pass to corrplot::corrplot() function.

See Also

Other signature plot: draw_sig_activity, draw_sig_profile, draw_subtypes_comparison

Examples

# NOT RUN {
# Load copy number signature
load(system.file("extdata", "toy_copynumber_signature.RData",
  package = "sigminer", mustWork = TRUE
))
sig_activity <- sig_get_activity(res$nmfObj)
sig_cor <- sig_get_correlation(sig_activity)
draw_sig_corrplot(sig_cor)
# }