make_balloon_plot_data_from_mtc: Make Balloon Plot from MTC Data structure

In cannin/tumorcomparer: Compare Patient Samples to Cell Line Models Using Molecular Data and Weighted Similarity

Make Balloon Plot from MTC Data structure

Description

Code to convert the processed output of TC over a pan-cancer dataset balloon plots for a single cancer type ("current_cancer_type") MTC - The subset of TC's output on a pan-cancer dataest which contains results for matched cancer type, i.e. for each cell line, it rreports the results when compared to tumors of the same cancer type So, for example, if we run TC on 10 cancer types on a pan-cancer type, we get 10 sets of results, with each set containing the results of comparing one of the 10 cancer types to all cell lines From this, MTC extracts only the results where the cell line and tumors are of the same cancer type, using the other cell lines to derive ranks We use ranks to compare across cancer types, since the weights and score distributions are very different across data types and cancer types

Usage

make_balloon_plot_data_from_mtc(mtc, cancer_type, melt_data = TRUE)

Arguments

mtc	(NOTE: users should not make dataset; the dataset with results from manuscript is included in the package). a data.frame with the columns: Cell_Line_Name: Name of the cell line Cell_Line_Cancer_Type: Name of the cancer type of the cell line Tumor_Cancer_Type: TCGA abbreviation of cancer type for tumor samples Mean_Similarity_To_Tumors_AVG: TODO Mean_Similarity_To_Tumors_MUT: TODO Mean_Similarity_To_Tumors_CNA: TODO Mean_Similarity_To_Tumors_EXP: TODO AVGSIM_Zscores; MUTSIM_Zscores: TODO CNASIM_Zscores; EXPSIM_Zscores: TODO AVGSIM_Percentile_Ranks: TODO MUTSIM_Percentile_Ranks: % Rank by Mutation CNASIM_Percentile_Ranks: % Rank by Copy Number EXPSIM_Percentile_Ranks: % Rank by Expression Categorization: TODO AVGSIM_Zscores_wrt_Tumors: TODO MUTSIM_Zscores_wrt_Tumors: TODO CNASIM_Zscores_wrt_Tumors: TODO EXPSIM_Zscores_wrt_Tumors: TODO Mean_Similarity_To_All_Tumors_AVG: TODO Mean_Similarity_To_All_Tumors_MUT: TODO Mean_Similarity_To_All_Tumors_CNA: TODO Mean_Similarity_To_All_Tumors_EXP: TODO Average_Of_Percentile_Ranks: TODO Rank_of_Average_Of_Percentile_Ranks: % Rank by Avg % Ranks
cancer_type	a cancer type abbreviation found in the MTC column Cell_Line_Cancer_Type
melt_data	boolean, whether to apply reshape2::melt() to data.frame

Value

a ggplot object

Examples

mtc_file <- system.file("extdata", "mtc_results_20200331", "mtc_results_20200331_no_factors.rds", 
  package="tumorcomparer")
mtc <- readRDS(mtc_file)
dat <- make_balloon_plot_data_from_mtc(mtc, "BRCA")

cannin/tumorcomparer documentation built on Feb. 7, 2023, 3:13 p.m.