Creates Kaplan-Meier survival plots for a given signature or gene, with automatic cutoff determination. Generates three types of plots: optimal cutoff (best cutoff), tertile-based (3 groups), and median split (2 groups).
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 = NULL,
index = 1
)Arguments
- input_pdata
Data frame with survival data and signature scores.
- signature
Character string. Column name of the target signature.
- project
Character string. Project name for output. Default is `"KM"`.
- ID
Character string. Column name for sample IDs. Default is `"ID"`.
- time
Character string. Column name for survival time. Default is `"time"`.
- status
Character string. Column name for survival status. Default is `"status"`.
- time_type
Character string. Time unit (`"month"` or `"day"`). Default is `"month"`.
- break_month
Numeric or `"auto"`. Time axis breaks. Default is `"auto"`.
- cols
Character vector. Optional custom colors.
- palette
Character string. Color palette if `cols` not provided. Default is `"jama"`.
- show_col
Logical indicating whether to show colors. Default is `TRUE`.
- mini_sig
Character string. Label for low score group. Default is `"score"`.
- fig.type
Character string. File format. Default is `"png"`.
- save_path
Character string or `NULL`. Directory for saving plots. If `NULL`, plots are not saved. Default is `NULL`.
- index
Integer. Index for multiple plots. Default is `1`.
Value
A list containing:
- data
Processed input data with group assignments
- plots
Combined survival plots
Examples
if (FALSE) { # \dontrun{
tcga_stad_pdata <- load_data("tcga_stad_pdata")
sig_surv_plot(
input_pdata = tcga_stad_pdata,
signature = "TMEscore_plus",
time = "time",
status = "OS_status"
)
} # }