batch_sig_surv_plot: Batch Signature Survival Plot

In IOBR/IOBR: Immune Oncology Biological Research

Batch Signature Survival Plot

Description

This function generates survival plots for multiple projects based on input data and signature scores.

Usage

batch_sig_surv_plot(
  input_pdata,
  signature,
  ID = "ID",
  column_of_Project = "ProjectID",
  project = NULL,
  time = "time",
  status = "status",
  time_type = "day",
  break_month = "auto",
  palette = "jama",
  cols = NULL,
  mini_sig = "score",
  save_path = "Multiple-KM-plot",
  show_col = TRUE,
  fig.type = "pdf"
)

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.
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".
column_of_Project	A character string specifying the name of the column representing the project IDs. Default is "ProjectID".
project	A character string specifying the project name. Default is NULL.
time	A character string specifying the name of the column representing the time variable. Default is "time".
status	A character string specifying the name of the column representing the status variable. Default is "status".
time_type	A character string specifying the type of time variable. Default is "day".Options are "day" and "month".
break_month	A character string specifying the break interval for the time variable. Default is "auto".
palette	A character string specifying the color palette to be used for the plots. Default is "jama".
cols	A vector specifying custom colors for the plots. Default is NULL.
mini_sig	A character string specifying the minimum signature score. Default is "score".
save_path	A character string specifying the path where the plots will be saved. Default is "Multiple-KM-plot".
show_col	A logical value indicating whether to show colors in the plots. Default is TRUE.
fig.type	A character string specifying the file type for saving the plots. Default is "pdf".

Value

A data frame containing the combined data from all projects after survival analysis.

Author(s)

Dongqiang Zeng

Examples

# Loading TCGA-STAD microenvironment signature data
data("sig_stad", package = "IOBR")
# Generating survival plots for multiple projects
sig_stad <- as.data.frame(sig_stad)
result <- batch_sig_surv_plot(input_pdata = sig_stad, signature = "T.cells.CD8", ID = "ID", column_of_Project = "ProjectID", project = NULL,
                              time = "OS_time", status = "OS_status", time_type = "month", break_month = "auto", palette = "jama",
                              cols = NULL, mini_sig = "score", save_path = "Multiple-KM-plot", show_col = TRUE, fig.type = "pdf")
print(result)

IOBR/IOBR documentation built on April 3, 2025, 2:19 p.m.