Generates Kaplan-Meier survival plots for multiple projects or cohorts based on signature scores. Automatically determines optimal cutpoints for signature stratification and creates publication-ready survival curves.
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 = file.path(tempdir(), "Multiple-KM-plot"),
show_col = TRUE,
fig_type = "pdf"
)Arguments
- input_pdata
Data frame containing survival data and signature scores.
- signature
Character string specifying the column name of the target signature for survival analysis.
- id
Character string specifying the column name containing unique identifiers. Default is `"ID"`.
- column_of_project
Character string specifying the column name containing project identifiers. Default is `"ProjectID"`.
- project
Character string or vector specifying project name(s) to analyze. If `NULL`, all projects are analyzed. Default is `NULL`.
- time
Character string specifying the column name containing time-to-event data. Default is `"time"`.
- status
Character string specifying the column name containing event status. Default is `"status"`.
- time_type
Character string specifying the time unit. Options are `"day"` or `"month"`. Default is `"day"`.
- break_month
Numeric value or `"auto"` specifying the interval for time axis breaks in months. Default is `"auto"`.
- palette
Character string specifying the color palette. Default is `"jama"`.
- cols
Character vector of custom colors. If `NULL`, palette is used. Default is `NULL`.
- mini_sig
Character string for the signature label in the legend. Default is `"score"`.
- save_path
Character string specifying the directory path for saving plots.
- show_col
Logical indicating whether to display color information. Default is `TRUE`.
- fig_type
Character string specifying the output file format (`"pdf"`, `"png"`, etc.). Default is `"pdf"`.
Examples
if (FALSE) { # \dontrun{
sig_stad <- load_data("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",
show_col = TRUE,
fig_type = "pdf"
)
} # }