Jens Sauer
f919a31527
This function loads the data and adjust some wrong column types. It shoulb be used from all other scripts to load the data. It the same source data for all following calculations. The data is stored inside a 'tibble' from the 'tidyverse' package.
76 lines
2.5 KiB
R
76 lines
2.5 KiB
R
# secMalASCT utilities
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#
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# License: GPL version 3
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# Jens Mathis Sauer (c) 2020
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library(tidyverse)
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#
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# Write plot to filename
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#
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# This will plot "fun" with arguments "..." as filetype "ftype" and
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# the output to "filename". Title and legends can be passed as list,
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# or NULL if not needed.
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# Default filesize is 3000x3000 px and 300 dpi resolution.
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#
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sma_plot_file <- function(fname, ftype, title_list, legend_list, fun, ...) {
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# Open file for writing
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ftype(filename = fname, width = 3000, height = 3000, res = 300)
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# run "fun" with passed arguments
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do.call(fun, list(...))
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if (!is.null(title_list)) {
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do.call(title, title_list)
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}
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if(!is.null(legend_list)) {
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do.call(legend, legend_list)
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}
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# hide "null device 1" in garbage
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garbage <- dev.off()
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}
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#
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# Load secMalASCT data
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#
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# This loads the secMalASCT data from a CSV file and adjusts some
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# columns to the correct type.
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#
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sma_load_data <- function(file) {
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sma <- as_tibble(read.csv(file, header = TRUE))
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# Type adjustments
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sma$follow_up_multi <- as.logical(sma$follow_up_multi)
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sma$nicotin_history <- as.logical(sma$nicotin_history)
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sma$relapse_treatment_asct <- as.logical(sma$relapse_treatment_asct)
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sma$relapse_treatment_chemotherapy <- as.logical(sma$relapse_treatment_chemotherapy)
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sma$relapse_treatment_radiotherapy <- as.logical(sma$relapse_treatment_radiotherapy)
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sma$relapse_treatment_surgery <- as.logical(sma$relapse_treatment_surgery)
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sma$pre_rt <- as.logical(sma$pre_rt)
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sma$pre_rt_type <- as.factor(sma$pre_rt_type)
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sma$post_rt <- as.logical(sma$post_rt)
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sma$post_rt_type <- as.factor(sma$post_rt_type)
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sma$pre_alkylating_agents <- as.logical(sma$pre_alkylating_agents)
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sma$pre_topoisomerase <- as.logical(sma$pre_topoisomerase)
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sma$pre_anthracyclines <- as.logical(sma$pre_anthracyclines)
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sma$peri_alkylating_agents <- as.logical(sma$peri_alkylating_agents)
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sma$peri_topoisomerase <- as.logical(sma$peri_topoisomerase)
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sma$peri_anthracyclines <- as.logical(sma$peri_anthracyclines)
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sma$post_alkylating_agents <- as.logical(sma$post_alkylating_agents)
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sma$post_topoisomerase <- as.logical(sma$post_topoisomerase)
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sma$post_anthracyclines <- as.logical(sma$post_anthracyclines)
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sma$maintenance_treatment <- as.logical(sma$maintenance_treatment)
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sma$maintenance_treatment_time <- as.integer(sma$maintenance_treatment_time)
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sma$maintenance_treatment_type <- as.factor(sma$maintenance_treatment_type)
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sma$thalidomid <- as.logical(sma$thalidomid)
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sma$bortezomib <- as.logical(sma$bortezomib)
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return(sma)
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}
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