run_surv_plot: Run survival analysis and plot using rpart output from...

In DonaghEgan/rpartSurvivalClassifier: Separates patients into high and low expression groups for a given gene and compares their survival outcomes.

Description

Run survival analysis and plot using rpart output from run_rpart()

Usage

run_surv_plot(
  clin_tb,
  gene_ids,
  surv_event,
  surv_time,
  expr_unit = "log2tpm",
  col_palette = NULL,
  print_pdf = NULL,
  title_text = "",
  sub_text = ""
)

Arguments

clin_tb	tibble created by run_rpart(), or a tibble containing a columns named 'gene_ids1_group' and surv_event, surv_time as below
gene_ids	vector of strings used in run_rpart to define gene used in classification
surv_event	colnames(clin_tb) relating to survival event
surv_time	colnames(clin_tb) relating to survival event
expr_unit	unit of expression in clin_tb; default - log2tpm
col_palette	colours to use in plotting (vector, high -> low expression; think palette in ggsurvplot is alphanum sorted...)
print_pdf	print PDF to file (else return in output list)
title_text	title text for plot
sub_text	sub text for plot

Value

table from survival::survdiff (log rank test), ggsurvplot PDF printed

Examples

expr_df <- readRDS(system.file("extdata", "expr_df.rds", package="rpartSurvivalClassifier"))
clin_df <- readRDS(system.file("extdata", "clin_df.rds", package="rpartSurvivalClassifier"))
clin_new_tb <- rpartSurvivalClassifier::run_rpart(expr_df = expr_df, gene_id = "CRABP2", clin_df = clin_df, surv_event = "OS", surv_time = "OS.time", join_el = "sample")
log_rank_res <- rpartSurvivalClassifier::run_surv_plot(clin_tb = clin_new_tb, gene_id = "CRABP2", surv_event = "OS", surv_time = "OS.time")

DonaghEgan/rpartSurvivalClassifier documentation built on Dec. 17, 2021, 5:29 p.m.