show_group_comparison: Plot Group Comparison Result

In sigminer: Extract, Analyze and Visualize Mutational Signatures for Genomic Variations

Plot Group Comparison Result

Description

Using result data from get_group_comparison, this function plots genotypes/phenotypes comparison between signature groups using ggplot2 package and return a list of ggplot object contains individual and combined plots. The combined plot is easily saved to local using cowplot::save_plot(). Of note, default fisher test p values are shown for categorical data and fdr values are shown for continuous data.

Usage

show_group_comparison(
  group_comparison,
  xlab = "group",
  ylab_co = NA,
  legend_title_ca = NA,
  legend_position_ca = "bottom",
  set_ca_sig_yaxis = FALSE,
  set_ca_custom_xlab = FALSE,
  show_pvalue = TRUE,
  ca_p_threshold = 0.01,
  method = "wilcox.test",
  p.adjust.method = "fdr",
  base_size = 12,
  font_size_x = 12,
  text_angle_x = 30,
  text_hjust_x = 0.2,
  ...
)

Arguments

group_comparison	a list from result of get_group_comparison function.
xlab	lab name of x axis for all plots. if it is NA, remove title for x axis.
ylab_co	lab name of y axis for plots of continuous type data. Of note, this argument should be a character vector has same length as group_comparison, the location for categorical type data should mark with NA.
legend_title_ca	legend title for plots of categorical type data.
legend_position_ca	legend position for plots of categorical type data. Of note, this argument should be a character vector has same length as group_comparison, the location for continuous type data should mark with NA.
set_ca_sig_yaxis	if TRUE, use y axis to show signature proportion instead of variable proportion.
set_ca_custom_xlab	only works when set_ca_sig_yaxis is TRUE. If TRUE, set x labels using input xlab, otherwise variable names will be used.
show_pvalue	if TRUE, show p values.
ca_p_threshold	a p threshold for categorical variables, default is 0.01. A p value less than 0.01 will be shown as P < 0.01.
method	a character string indicating which method to be used for comparing means. It can be 't.test', 'wilcox.test' etc..
p.adjust.method	correction method, default is 'fdr'. Run p.adjust.methods to see all available options.
base_size	overall font size.
font_size_x	font size for x.
text_angle_x	text angle for x.
text_hjust_x	adjust x axis text
...	other paramters pass to ggpubr::compare_means() or ggpubr::stat_compare_means() according to the specified method.

Value

a list of ggplot objects.

Author(s)

Shixiang Wang [e-mail]

Examples

load(system.file("extdata", "toy_copynumber_signature_by_W.RData",
  package = "sigminer", mustWork = TRUE
))

# Assign samples to clusters
groups <- get_groups(sig, method = "k-means")

set.seed(1234)

groups$prob <- rnorm(10)
groups$new_group <- sample(c("1", "2", "3", "4", NA), size = nrow(groups), replace = TRUE)

# Compare groups (filter NAs for categorical coloumns)
groups.cmp <- get_group_comparison(groups[, -1],
  col_group = "group",
  cols_to_compare = c("prob", "new_group"),
  type = c("co", "ca"), verbose = TRUE
)

# Compare groups (Set NAs of categorical columns to 'Rest')
groups.cmp2 <- get_group_comparison(groups[, -1],
  col_group = "group",
  cols_to_compare = c("prob", "new_group"),
  type = c("co", "ca"), NAs = "Rest", verbose = TRUE
)

show_group_comparison(groups.cmp)

ggcomp <- show_group_comparison(groups.cmp2)
ggcomp$co_comb
ggcomp$ca_comb

sigminer documentation built on May 29, 2024, 3:11 a.m.