refactored dm om plots and generated the final layout
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28510471f0
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5bdfd03443
5 changed files with 169 additions and 85 deletions
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@ -196,11 +196,11 @@ corr_df_m3_f = corr_data_extract(merged_df3
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, extract_scaled_cols = F)
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head(corr_df_m3_f)
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corr_df_m2_f = corr_data_extract(merged_df2
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, gene = gene
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, drug = drug
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, extract_scaled_cols = F)
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head(corr_df_m2_f)
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# corr_df_m2_f = corr_data_extract(merged_df2
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# , gene = gene
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# , drug = drug
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# , extract_scaled_cols = F)
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# head(corr_df_m2_f)
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s4 = c("\nSuccessfully sourced Corr_data.R")
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cat(s4)
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@ -76,8 +76,9 @@ lf_duetP$param_type = factor(lf_duetP$param_type)
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table(lf_duetP$param_type)
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duetP = lf_bp2(lf_duetP
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 0.2)
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#==============
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# Plot:FoldX
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@ -89,8 +90,9 @@ lf_foldxP$param_type = factor(lf_foldxP$param_type)
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table(lf_foldxP$param_type)
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foldxP = lf_bp2(lf_foldxP
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 0.1)
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#==============
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# Plot:DeepDDG
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@ -102,9 +104,10 @@ lf_deepddgP$param_type = factor(lf_deepddgP$param_type)
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table(lf_deepddgP$param_type)
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deepddgP = lf_bp2(lf_deepddgP
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 0.3)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 0.2)
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deepddgP
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#==============
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@ -117,8 +120,10 @@ lf_dynamut2P$param_type = factor(lf_dynamut2P$param_type)
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table(lf_dynamut2P$param_type)
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dynamut2P = lf_bp2(lf_dynamut2P
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 0.2)
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#==============
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# Plot:ConSurf
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@ -130,8 +135,8 @@ lf_consurfP$param_type = factor(lf_consurfP$param_type)
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table(lf_consurfP$param_type)
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consurfP = lf_bp2(lf_consurfP
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F)
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#==============
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# Plot:SNAP2
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@ -143,8 +148,8 @@ lf_snap2P$param_type = factor(lf_snap2P$param_type)
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table(lf_snap2P$param_type)
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snap2P = lf_bp2(lf_snap2P
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F)
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#==============
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# Plot:PROVEAN
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@ -156,12 +161,13 @@ lf_proveanP$param_type = factor(lf_proveanP$param_type)
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table(lf_proveanP$param_type)
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proveanP = lf_bp2(lf_proveanP
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F)
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#==============
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############################################################################
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#================
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# Plot: mCSM-lig
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#==============
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#================
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lf_mcsm_ligP = all_dm_om_df[['lf_mcsm_lig']]
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#lf_mcsm_ligP = lf_mcsm_lig[!lf_mcsm_lig$param_type%in%c(static_colsP),]
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table(lf_mcsm_ligP$param_type)
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@ -169,12 +175,30 @@ lf_mcsm_ligP$param_type = factor(lf_mcsm_ligP$param_type)
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table(lf_mcsm_ligP$param_type)
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mcsmligP = lf_bp2(lf_mcsm_ligP
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 1)
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#==============
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#=================
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# Plot: mmCSM-lig2
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#=================
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lf_mmcsm_lig2P = all_dm_om_df[['lf_mmcsm_lig2']]
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#lf_mmcsm_lig2P = lf_mmcsm_lig2P[!lf_mmcsm_lig2P$param_type%in%c(static_colsP),]
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table(lf_mmcsm_lig2P$param_type)
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lf_mmcsm_lig2P$param_type = factor(lf_mmcsm_lig2P$param_type)
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table(lf_mmcsm_lig2P$param_type)
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mcsmlig2P = lf_bp2(lf_mmcsm_lig2P
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 1)
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mcsmlig2P
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#================
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# Plot: mCSM-ppi2
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#==============
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#================
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if (tolower(gene)%in%geneL_ppi2){
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lf_mcsm_ppi2P = all_dm_om_df[['lf_mcsm_ppi2']]
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#lf_mcsm_ppi2P = lf_mcsm_ppi2[!lf_mcsm_ppi2$param_type%in%c(static_colsP),]
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@ -183,8 +207,10 @@ if (tolower(gene)%in%geneL_ppi2){
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table(lf_mcsm_ppi2P$param_type)
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mcsmppi2P = lf_bp2(lf_mcsm_ppi2P
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 1)
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}
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#==============
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@ -198,28 +224,39 @@ if (tolower(gene)%in%geneL_na){
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table(lf_mcsm_naP$param_type)
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mcsmnaP = lf_bp2(lf_mcsm_naP
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#, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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#, p_title = ""
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, violin_quantiles = c(0.5), monochrome = F
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, dot_transparency = 1)
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}
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######################################
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# Outplot with stats
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######################################
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outdir_images = paste0("~/git/Writing/thesis/images/results/", tolower(gene), "/")
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dm_om_combinedP = paste0(outdir_images
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,tolower(gene)
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,"_dm_om_all.svg" )
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cat("DM OM plots with stats:", dm_om_combinedP)
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svg(dm_om_combinedP, width = 32, height = 18)
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cowplot::plot_grid(
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cowplot::plot_grid(duetP, foldxP, deepddgP, dynamut2P, genomicsP, distanceP
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, nrow=1),
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# cowplot::plot_grid(genomicsP, distanceP
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# , nrow = 1),
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, nrow=1
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, rel_widths = c(1/7, 1/7,1/7,1/7, 1/7, 1.75/7)),
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#, rel_widths = c(1/8, 1/8,1/8,1/8, 1/8, 2.75/8)), # for 3 distances
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cowplot::plot_grid(consurfP, snap2P, proveanP
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, mcsmligP
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, mcsmlig2P
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, mcsmppi2P
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#, mcsmnaP
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, nrow=1),
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nrow=2)
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dev.off()
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foo = lf_consurfP
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#foo = lf_consurfP
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# proveanP = lf_bp2(lf_proveanP, colour_categ = "mutation_info_labels"
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# , p_title = paste0("Evolutionary conservation")
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@ -8,6 +8,11 @@ source("~/git/LSHTM_analysis/config/embb.R")
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# get plottting dfs
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source("~/git/LSHTM_analysis/scripts/plotting/get_plotting_dfs.R")
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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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###################################################################
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# FIXME: ADD distance to NA when SP replies
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# DONE: plotting_globals.R
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@ -86,12 +91,6 @@ all_cols = c(common_cols
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, scaled_cols_conservation
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, outcome_cols_conservation)
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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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####################################
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# merged_df3: NECESSARY pre-processing
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###################################
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