74 lines
3.2 KiB
R
74 lines
3.2 KiB
R
#source("~/git/LSHTM_analysis/config/pnca.R")
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#source("~/git/LSHTM_analysis/config/alr.R")
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#source("~/git/LSHTM_analysis/config/gid.R")
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source("~/git/LSHTM_analysis/config/embb.R")
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#source("~/git/LSHTM_analysis/config/katg.R")
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#source("~/git/LSHTM_analysis/config/rpob.R")
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#########################################################
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# TASK: Generate averaged stability values by position
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# calculated across all stability tools
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# for a given structure
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#########################################################
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#=======
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# output
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#=======
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outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene))
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outfile_mean_ens_st_aff = paste0(outdir_images, "/", tolower(gene)
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, "_mean_ens_stability.csv")
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print(paste0("Output file:", outfile_mean_ens_st_aff))
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#%%===============================================================
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#=============
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# Input: merged_df3
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#=============
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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#merged_df3= paste0("/home/tanu/git/Data/", drug, "/output/", tolower(gene), "_merged_df3.csv")
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cols_to_extract_ms = c("mutationinformation", "position", "avg_stability_scaled")
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df3 = merged_df3[, cols_to_extract_ms]
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length(df3$mutationinformation)
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# ensemble average of predictors by position
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avg_stability_by_position <- df3 %>%
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dplyr::group_by(position) %>%
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dplyr::summarize(avg_stability_scaled_pos = mean(avg_stability_scaled))
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min(avg_stability_by_position$avg_stability_scaled_pos)
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max(avg_stability_by_position$avg_stability_scaled_pos)
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avg_stability_by_position['avg_stability_scaled_pos_scaled'] = lapply(avg_stability_by_position['avg_stability_scaled_pos']
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, function(x) {
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scales::rescale_mid(x, to = c(-1,1)
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#, from = c(en_stab_min,en_stab_max))
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, mid = 0
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, from = c(0,1))
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})
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cat(paste0('Average stability scores:\n'
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, head(avg_stability_by_position['avg_stability_scaled_pos'])
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, '\n---------------------------------------------------------------'
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, '\nAverage stability scaled scores:\n'
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, head(avg_stability_by_position['avg_stability_scaled_pos_scaled'])
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))
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all(avg_stability_by_position['avg_stability_scaled_pos'] == avg_stability_by_position['avg_stability_scaled_pos_scaled'])
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# convert to a data frame
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avg_stability_by_position = as.data.frame(avg_stability_by_position)
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##################################################################
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# output
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#write.csv(combined_df, outfile_mean_ens_st_aff
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write.csv(avg_stability_by_position
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, outfile_mean_ens_st_aff
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, row.names = F)
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cat("Finished writing file:\n"
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, outfile_mean_ens_st_aff
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, "\nNo. of rows:", nrow(avg_stability_by_position)
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, "\nNo. of cols:", ncol(avg_stability_by_position))
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# end of script
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#===============================================================
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