sig_surv_plot: Multiple survival KM-plot to a signature or gene

In IOBR/IOBR: Immune Oncology Biological Research

Multiple survival KM-plot to a signature or gene

Description

Multiple survival KM-plot to a signature or gene

Usage

sig_surv_plot(
  input_pdata,
  signature,
  project = "KM",
  ID = "ID",
  time = "time",
  status = "status",
  time_type = "month",
  break_month = "auto",
  cols = NULL,
  palette = "jama",
  show_col = TRUE,
  mini_sig = "score",
  fig.type = "png",
  save_path = "KM-plot",
  index = 1
)

Arguments

input_pdata	This parameter represents the input data for the survival analysis. It is expected to be a data frame.
signature	This parameter specifies the column name in input_pdata that represents the target signature for survival analysis.
project	This optional parameter represents the project name. The default value is "KM".
ID	This optional parameter represents the column name in input_pdata that contains the unique identifier for each data point. The default value is "ID".
time	This optional parameter represents the column name in input_pdata that contains the time variable for survival analysis. The default value is "time".
status	This optional parameter represents the column name in input_pdata that contains the survival status variable. The default value is "status".
time_type	This optional parameter specifies the time unit used in the analysis. The default value is "month".
break_month	This optional parameter specifies the interval at which the time axis breaks should be made in the Kaplan-Meier plot. The default value is "auto".
cols	This optional parameter allows the user to specify the color palette for the plot. If not specified, a default palette will be used.
palette	This optional parameter allows the user to specify the palette type if cols is not provided. The default value is "jama".
show_col	logical variable, if TRUE, color will be print and show in the R studio
mini_sig	This optional parameter represents the label for the mini signature in the legend. The default value is "score".
fig.type	This optional parameter specifies the file format for saving the plot. The default value is "png".
save_path	This optional parameter specifies the directory path for saving the plot. The default value is "KM-plot".
index	This parameter represents the index for multiple plots generated in a single run. It is used as the prefix in the filename. The default value is 1.

Value

survival

Author(s)

Dongqiang Zeng

Examples

data("tcga_stad_pdata", package = "IOBR")
sig_surv_plot(input_pdata = tcga_stad_pdata, signature = "TMEscore_plus", time = "time", status = "OS_status")

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.