65 lines
2.5 KiB
R
65 lines
2.5 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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# ONLY ONCE
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#source("~/git/LSHTM_analysis/config/pnca.R")
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#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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#write.csv(colnames(merged_df3), "data_colnames.csv")
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#---------------------------------------------------
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colnames_order_pnca = read.csv("~/git/ML_AI_training/ml_data/colnames_order.csv"
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, header = F)
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# reorder columns by name
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colnames_order_pnca <- colnames_order_pnca$V1
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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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#source("~/git/LSHTM_analysis/config/alr.R")
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# FIXME: "cycloserine" "mcsm_ppi2_affinity" "mcsm_ppi2_scaled" "mcsm_ppi2_outcome" "interface_dist"
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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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mdf3_outName = paste0(outdir, "/", tolower(gene), "_merged_df3.csv")
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mdf3_outName
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if( (length(colnames_order) == ncol(merged_df3)) && (all(colnames_order %in%colnames(merged_df3))) ){
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cat("\nProceeding with rearranging columns in merged_df3")
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merged_df3_o = merged_df3[ , colnames_order]
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cat("\nWriting output file:", mdf3_outName)
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write.csv(merged_df3_o, mdf3_outName, row.names = F)
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cat("\nnrows:" , nrow(merged_df3_o)
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, "\nncols:" , ncol(merged_df3_o))
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}else
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cat("length mismatch:"
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, colnames(merged_df3)[!colnames(merged_df3)%in%(colnames_order )]
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)
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mdf2_outName = paste0(outdir, "/", tolower(gene), "_merged_df2.csv")
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mdf2_outName
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if( (length(colnames_order) == ncol(merged_df2)) && (all(colnames_order %in%colnames(merged_df2))) ){
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cat("\nProceeding with rearranging columns in merged_df3")
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merged_df2_o = merged_df2[ , colnames_order]
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cat("\nWriting output file:", mdf2_outName)
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write.csv(merged_df2_o, mdf2_outName, row.names = F)
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cat("\nnrows:" , nrow(merged_df2_o)
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, "\nncols:" , ncol(merged_df2_o))
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}
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