postTIPC_SurvivalAnalysis: Heat-map of TIPC metric color-coded by clustering results

In MPE-Lab/TIPC: Tumor-Immune Partitioning and Clustering (test)

Description

Plotting heat-maps of TIPC metric clustering results of all k's unless it is specified; using R package coxph

Usage

postTIPC_SurvivalAnalysis(
  root_dir = NULL,
  clustering_subfolder_nm = NULL,
  one_k = NULL,
  min_cluster_size = 30,
  method = c("univariate", "multivariate"),
  surv_data = NULL,
  ref_cluster_no = NULL,
  all_ref_check = FALSE,
  KM_xlab = "Time"
)

Arguments

root_dir	A directory path containing (1) the TIPC_metrics, i.e. normalized TIPC metrics of all 5 directions output from normalize_metrics; (2) the result folder of TIPC clustering results output from consensus_clustering.
clustering_subfolder_nm	A character string of sub-folder name generated during consensus_clustering, parked under root_dir.
one_k	An integer specifying the cluster number selected for heat-map plotting; otherwise all k's found under TIPC_cluster_dir will be processed.
min_cluster_size	An integer indicating the minimum size of TIPC cluster to be tested for survival analysis; default 10.
method	A character string indicating the method of survival analysis: univariate or multivariate.
surv_data	A data frame of size r rows x 2 (or more) columns: containing r tumors and minimum 2 variables with column names 'time' (numeric) and 'cens' (integer), any additional columns are used as covariates (factors) if multivariate analysis is chosen. NOTE: rownames containing tumor_ids.
ref_cluster_no	An integer indicating the cluster id to be used as the reference, if unspecified (NULL) cluster of largest size will be used.
all_ref_check	A boolean indicating if multiple survival analyses are performed using individual clusters as reference; if TRUE, it will overwrite ref_cluster_no
KM_xlab	A character string specifying the x-axis label of Kaplan-Meier curve

MPE-Lab/TIPC documentation built on Sept. 17, 2021, 6:33 p.m.