plot_SMC: Plot results of the Stratification of a Mutational Catalogue

In slw287r/yapsa: Yet Another Package for Signature Analysis

Description

Plot a big composite figure with 3 columns: in the left column the per-PID absolute exposures will be shown, in the middle column the per_PID relative or normalized exposures will be shown, in the right column the cohort-wide exposures are shown (averaged over PIDs).

Usage

plot_SMC(
  number_of_strata,
  output_path,
  decomposition_method,
  number_of_sigs,
  name_list,
  exposures_strata_list,
  this_signatures_ind_df,
  this_subgroups_df,
  in_strata_order_ind,
  exposures_both_rel_df_list,
  cohort_method_flag,
  fig_width = 1200,
  fig_height = 900,
  fig_type = "png",
  in_label_orientation = "turn",
  this_sum_ind = NULL
)

Arguments

number_of_strata	Number of strata as deduced from link{SMC}
output_path	Path to file where the results are going to be stored. If NULL, the results will be plotted to the running environment.
decomposition_method	String for the filename of the generated barplot.
number_of_sigs	Number of signatures
name_list	Names of the contructed strata.
exposures_strata_list	The list of s strata specific exposures Hi, all are numerical data frames with l rows and m columns, l being the number of signatures and m being the number of samples
this_signatures_ind_df	A data frame containing meta information about the signatures
this_subgroups_df	A data frame indicating which PID (patient or sample identifyier) belongs to which subgroup
in_strata_order_ind	Index vector defining reordering of the strata
exposures_both_rel_df_list	A list of s strata specific cohortwide (i.e. averaged over cohort) normalized exposures
cohort_method_flag	Either or several of c("all_PIDs","cohort","norm_PIDs"), representing alternative ways to average over the cohort.
fig_width	Width of the figure to be plotted
fig_height	Height of the figure to be plotted
fig_type	png or pdf
in_label_orientation	Whether or not to turn the labels on the x-axis.
this_sum_ind	Optional set of indices for reordering the PIDs

Value

The function doesn't return any value.

Examples

NULL

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