Jens Sauer
c68e536861
The minimum age for this study is 16.0 years or older at time of transplantation.
86 lines
2.7 KiB
R
86 lines
2.7 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, 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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#
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# Write plot into variable, then printing it manually. This is
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# needed to save plots from package "survminer" at the moment.
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#
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# See: https://github.com/kassambara/survminer/issues/152
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#
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p <- fun()
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print(p)
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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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#
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# Limit to patients which are at least 16.0 years old at time
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# of transplantation.
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sma <- filter(sma, asct_age >= 16.0)
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return(sma)
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}
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#
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# Global break.time.by value
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#
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sma_break.time.by = 5 * 365.25
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