46 lines
1.7 KiB
R
46 lines
1.7 KiB
R
#!/usr/bin/env Rscript
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# target var options:
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# drtype: MDR, etc, full data
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# pyrazinamide: 0 and 1, loss of data
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# mutation_info_labels: DM and OM, full data
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##################################################
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###################################################
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#config_gene = c("alr", "embb", "gid", "katg", "pnca", "rpob")
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#config_gene = c("alr", "embb")
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#sapply(config_gene, function(x) source(paste0("~/git/LSHTM_analysis/config/", x, ".R")), USE.NAMES = F)
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#----------------------------------------------------
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#source("~/git/LSHTM_analysis/config/alr.R")
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#source("~/git/LSHTM_analysis/config/embb.R")
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#source("~/git/LSHTM_analysis/config/gid.R")
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#source("~/git/LSHTM_analysis/config/katg.R")
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#source("~/git/LSHTM_analysis/config/pnca.R")
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source("~/git/LSHTM_analysis/config/rpob.R")
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#----------------------------------------------------
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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######################################################
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gene; drug
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merged_df3$active_aa_pos = ifelse(merged_df3$position %in% active_aa_pos , 1, 0)
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table(merged_df3$active_aa_pos)
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mdf3_outName = paste0(outdir, "/", tolower(gene), "_merged_df3.csv")
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mdf3_outName
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cat("\nWriting output file:", mdf3_outName)
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write.csv(merged_df3, mdf3_outName, row.names = F)
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cat("\nnrows:" , nrow(merged_df3)
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, "\nncols:" , ncol(merged_df3))
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#=========================================================
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merged_df2$active_aa_pos = ifelse(merged_df2$position %in% active_aa_pos , 1, 0)
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table(merged_df2$active_aa_pos)
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mdf2_outName = paste0(outdir, "/", tolower(gene), "_merged_df2.csv")
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mdf2_outName
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cat("\nWriting output file:", mdf2_outName)
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write.csv(merged_df2, mdf2_outName, row.names = F)
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cat("\nnrows:" , nrow(merged_df2)
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, "\nncols:" , ncol(merged_df2))
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