added count for targets for all genes and ran multiple classification models for all of the genes and target as a start
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commit
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8 changed files with 948 additions and 0 deletions
335
ml_data/.Rhistory
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335
ml_data/.Rhistory
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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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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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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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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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###################################################
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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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active_aa_pos
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merged_df3['position']%in%active_aa_pos
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merged_df3$position%in%active_aa_pos
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merged_df3['active_aa_pos'] <- merged_df3['position']
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merged_df3['active_aa_pos']
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identical(merged_df3['active_aa_pos'] , merged_df3['position'])
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(merged_df3['active_aa_pos'] == merged_df3['position'])
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all(merged_df3['active_aa_pos'] == merged_df3['position'])
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merged_df3['active_aa_pos'] <- merged_df3['position']
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if (merged_df3$position%in%active_aa_pos){
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merged_df3['active_aa_pos'] = 1
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}else{
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merged_df3['active_aa_pos'] = 0
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}
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merged_df3['active_aa_pos']
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table(merged_df3$active_aa_pos)
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merged_df3['active_aa_pos'] <- merged_df3['position']
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merged_df3$active_aa_pos <- merged_df3$osition
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merged_df3$active_aa_pos
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merged_df3$active_aa_pos <- merged_df3$position
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merged_df3$active_aa_pos
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merged_df3$postion%in%active_aa_pos
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merged_df3$postion%in%active_aa_pos
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merged_df3$postion
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erged_df3$position%in%active_aa_pos
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merged_df3$position
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active_aa_pos
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which(merged_df3$position%in%active_aa_pos)
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c =which(merged_df3$position%in%active_aa_pos)
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merged_df3$position[c]
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active_aa_pos
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merged_df3$position%in%active_aa_pos
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merged_df3$active_aa_pos <- merged_df3$position
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merged_df3$active_aa_pos %in% active_aa_pos
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ifelse(merged_df3$active_aa_pos %in% active_aa_pos , "1", "0")
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table(merged_df3$active_aa_po)
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str(merged_df3$active_aa_po)
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str(merged_df3$active_aa_pos)
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#TODO later!
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merged_df3$active_aa_pos <- merged_df3$position
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merged_df3$active_aa_pos
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ifelse(merged_df3$active_aa_pos %in% active_aa_pos , 1, 0)
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str(merged_df3$active_aa_pos)
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#str(merged_df3$active_aa_pos)
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table(merged_df3$active_aa_pos)
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#str(merged_df3$active_aa_pos)
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foo = merged_df3$active_aa_pos
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merged_df3$active_aa_pos
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ifelse(merged_df3$active_aa_pos %in% active_aa_pos , 1, 0)
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merged_df3$active_aa_pos = ifelse(merged_df3$position %in% active_aa_pos , 1, 0)
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#str(merged_df3$active_aa_pos)
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foo = merged_df3$active_aa_pos
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#str(merged_df3$active_aa_pos)
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table(merged_df3$active_aa_pos)
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length(active_aa_pos)
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which(merged_df3$position%in%active_aa_pos)
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which(merged_df3$position%in%active_aa_pos)
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which(!merged_df3$position%in%active_aa_pos)
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which(merged_df3$position%in%active_aa_pos)
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active_aa_pos)
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active_aa_pos
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merged_df3$position[209,]
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merged_df3[209,]
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merged_df3$position[209]
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merged_df3[209]
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merged_df3[209,]
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active_aa_pos
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merged_df3$position[!merged_df3$position%in%active_aa_pos]
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merged_df3$position[!active_aa_pos%in%merged_df3$position]
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active_aa_pos
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active_aa_pos[!active_aa_pos%in%merged_df3$position]
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#str(merged_df3$active_aa_pos)
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table(merged_df3$active_aa_pos)
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###################################################
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#config_gene = c("alr", "embb", "gid", "katg", "pnca", "rpob")
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#config_gene = c("alr", "embb")
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#sapply(config_gene, function(x) source(paste0("~/git/LSHTM_analysis/config/", x, ".R")), USE.NAMES = F)
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#----------------------------------------------------
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# source("~/git/LSHTM_analysis/config/alr.R")
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source("~/git/LSHTM_analysis/config/embb.R")
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# source("~/git/LSHTM_analysis/config/gid.R")
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# source("~/git/LSHTM_analysis/config/katg.R")
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# source("~/git/LSHTM_analysis/config/pnca.R")
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# source("~/git/LSHTM_analysis/config/rpob.R")
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#----------------------------------------------------
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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merged_df3$active_aa_pos = ifelse(merged_df3$position %in% active_aa_pos , 1, 0)
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#str(merged_df3$active_aa_pos)
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table(merged_df3$active_aa_pos)
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cat("\nWriting output file:", mdf3_outName)
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write.csv(merged_df3, mdf3_outName, row.names = F)
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cat("\nnrows:" , nrow(merged_df3)
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, "\nncols:" , ncol(merged_df3))
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merged_df2$active_aa_pos = ifelse(merged_df2$position %in% active_aa_pos , 1, 0)
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table(merged_df3$active_aa_pos)
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table(merged_df2$active_aa_pos)
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###################################################
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#config_gene = c("alr", "embb", "gid", "katg", "pnca", "rpob")
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#config_gene = c("alr", "embb")
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#sapply(config_gene, function(x) source(paste0("~/git/LSHTM_analysis/config/", x, ".R")), USE.NAMES = F)
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#----------------------------------------------------
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# source("~/git/LSHTM_analysis/config/alr.R")
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source("~/git/LSHTM_analysis/config/embb.R")
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# source("~/git/LSHTM_analysis/config/gid.R")
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# source("~/git/LSHTM_analysis/config/katg.R")
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# source("~/git/LSHTM_analysis/config/pnca.R")
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# source("~/git/LSHTM_analysis/config/rpob.R")
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#----------------------------------------------------
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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######################################################
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merged_df3$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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###################################################
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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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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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###################################################
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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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gene
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drug
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######################################################
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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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###################################################
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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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###################################################
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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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###################################################
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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)
|
||||
cat("\nnrows:" , nrow(merged_df3)
|
||||
, "\nncols:" , ncol(merged_df3))
|
||||
#=========================================================
|
||||
merged_df2$active_aa_pos = ifelse(merged_df2$position %in% active_aa_pos , 1, 0)
|
||||
table(merged_df2$active_aa_pos)
|
||||
mdf2_outName = paste0(outdir, "/", tolower(gene), "_merged_df2.csv")
|
||||
mdf2_outName
|
||||
cat("\nWriting output file:", mdf2_outName)
|
||||
write.csv(merged_df2, mdf2_outName, row.names = F)
|
||||
cat("\nnrows:" , nrow(merged_df2)
|
||||
, "\nncols:" , ncol(merged_df2))
|
||||
65
ml_data/del/ml_data_v1.R
Normal file
65
ml_data/del/ml_data_v1.R
Normal file
|
|
@ -0,0 +1,65 @@
|
|||
#!/usr/bin/env Rscript
|
||||
|
||||
# target var options:
|
||||
# drtype: MDR, etc, full data
|
||||
# pyrazinamide: 0 and 1, loss of data
|
||||
# mutation_info_labels: DM and OM, full data
|
||||
##################################################
|
||||
# ONLY ONCE
|
||||
#source("~/git/LSHTM_analysis/config/pnca.R")
|
||||
#source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
|
||||
#write.csv(colnames(merged_df3), "data_colnames.csv")
|
||||
#---------------------------------------------------
|
||||
colnames_order_pnca = read.csv("~/git/ML_AI_training/ml_data/colnames_order.csv"
|
||||
, header = F)
|
||||
# reorder columns by name
|
||||
colnames_order_pnca <- colnames_order_pnca$V1
|
||||
###################################################
|
||||
#config_gene = c("alr", "embb", "gid", "katg", "pnca", "rpob")
|
||||
#config_gene = c("alr", "embb")
|
||||
#sapply(config_gene, function(x) source(paste0("~/git/LSHTM_analysis/config/", x, ".R")), USE.NAMES = F)
|
||||
|
||||
#source("~/git/LSHTM_analysis/config/alr.R")
|
||||
# FIXME: "cycloserine" "mcsm_ppi2_affinity" "mcsm_ppi2_scaled" "mcsm_ppi2_outcome" "interface_dist"
|
||||
# source("~/git/LSHTM_analysis/config/embb.R")
|
||||
# source("~/git/LSHTM_analysis/config/gid.R")
|
||||
# source("~/git/LSHTM_analysis/config/katg.R")
|
||||
source("~/git/LSHTM_analysis/config/pnca.R")
|
||||
# source("~/git/LSHTM_analysis/config/rpob.R")
|
||||
##################################################
|
||||
source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
|
||||
|
||||
######################################################
|
||||
mdf3_outName = paste0(outdir, "/", tolower(gene), "_merged_df3.csv")
|
||||
mdf3_outName
|
||||
|
||||
if( (length(colnames_order) == ncol(merged_df3)) && (all(colnames_order %in%colnames(merged_df3))) ){
|
||||
cat("\nProceeding with rearranging columns in merged_df3")
|
||||
merged_df3_o = merged_df3[ , colnames_order]
|
||||
cat("\nWriting output file:", mdf3_outName)
|
||||
write.csv(merged_df3_o, mdf3_outName, row.names = F)
|
||||
cat("\nnrows:" , nrow(merged_df3_o)
|
||||
, "\nncols:" , ncol(merged_df3_o))
|
||||
|
||||
}else
|
||||
cat("length mismatch:"
|
||||
, colnames(merged_df3)[!colnames(merged_df3)%in%(colnames_order )]
|
||||
)
|
||||
|
||||
mdf2_outName = paste0(outdir, "/", tolower(gene), "_merged_df2.csv")
|
||||
mdf2_outName
|
||||
|
||||
if( (length(colnames_order) == ncol(merged_df2)) && (all(colnames_order %in%colnames(merged_df2))) ){
|
||||
cat("\nProceeding with rearranging columns in merged_df3")
|
||||
merged_df2_o = merged_df2[ , colnames_order]
|
||||
cat("\nWriting output file:", mdf2_outName)
|
||||
write.csv(merged_df2_o, mdf2_outName, row.names = F)
|
||||
cat("\nnrows:" , nrow(merged_df2_o)
|
||||
, "\nncols:" , ncol(merged_df2_o))
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
Loading…
Add table
Add a link
Reference in a new issue