222 lines
7.1 KiB
R
222 lines
7.1 KiB
R
geneL_normal = c("pnca")
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geneL_na = c("gid", "rpob")
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geneL_ppi2 = c("alr", "embb", "katg", "rpob")
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if (tolower(gene)%in%geneL_na){
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lf_mcsm_na
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}
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if (tolower(gene)%in%geneL_ppi2){
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lf_mcsm_ppi2
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}
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colnames(lf_duet)
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table(lf_duet$param_type)
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static_colsP = c("Lig Dist(Å)","ASA", "RSA","RD","KD","Log10(MAF)")
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stability_suffix <- paste0(delta_symbol, delta_symbol, "G")
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lf_commonP = lf_duet[!lf_duet$param_type%in%c("DUET ΔΔG"),]
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lf_commonP$param_type = levels(droplevels(lf_commonP$param_type))
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table(lf_commonP$param_type); colnames(lf_commonP)
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lf_commonP$outcome = lf_commonP$duet_outcome
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lf_commonP$duet_outcome = NULL
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lf_duet$outcome = lf_duet$duet_outcome
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lf_duet$duet_outcome = NULL
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lf_duetP = lf_duet[!lf_duet$param_type%in%c(static_colsP, "outcome"),]
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lf_duetP$param_type = levels(droplevels(lf_duetP$param_type))
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table(lf_duetP$param_type); colnames(lf_duetP)
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colnames(lf_duetP)
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lf_foldx$outcome = lf_foldx$foldx_outcome
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lf_foldx$foldx_outcome = NULL
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lf_foldxP = lf_foldx[!lf_foldx$param_type%in%c(static_colsP,"outcome"),]
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lf_foldxP$param_type = levels(droplevels(lf_foldxP$param_type))
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table(lf_foldxP$param_type)
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colnames(lf_foldxP)
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lf_deepddg$outcome = lf_deepddg$deepddg_outcome
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lf_deepddg$deepddg_outcome = NULL
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lf_deepddgP = lf_deepddg[!lf_deepddg$param_type%in%c(static_colsP, "outcome"),]
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lf_deepddgP$param_type = levels(droplevels(lf_deepddgP$param_type))
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table(lf_deepddgP$param_type)
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colnames(lf_deepddgP)
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lf_dynamut2$outcome = lf_dynamut2$ddg_dynamut2_outcome
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lf_dynamut2$ddg_dynamut2_outcome = NULL
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lf_dynamut2P = lf_dynamut2[!lf_dynamut2$param_type%in%c(static_colsP, "outcome"),]
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lf_dynamut2P$param_type = levels(droplevels(lf_dynamut2P$param_type))
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table(lf_dynamut2P$param_type)
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colnames(lf_dynamut2P)
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lf_consurf$outcome = lf_consurf$consurf_outcome
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lf_consurf$consurf_outcome = NULL
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lf_consurfP = lf_consurf[!lf_consurf$param_type%in%c(static_colsP),]
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lf_consurfP$param_type = levels(droplevels(lf_consurfP$param_type))
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table(lf_consurfP$param_type)
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colnames(lf_consurfP)
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lf_snap2$outcome = lf_snap2$snap2_outcome
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lf_snap2$snap2_outcome = NULL
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lf_snap2P = lf_snap2[!lf_snap2$param_type%in%c(static_colsP),]
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lf_snap2P$param_type = levels(droplevels(lf_snap2P$param_type))
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table(lf_snap2P$param_type)
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colnames(lf_snap2P)
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lf_provean$outcome = lf_provean$provean_outcome
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lf_provean$provean_outcome = NULL
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lf_proveanP = lf_provean[!lf_provean$param_type%in%c(static_colsP),]
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lf_proveanP$param_type = levels(droplevels(lf_proveanP$param_type))
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table(lf_proveanP$param_type)
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colnames(lf_proveanP)
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bar = rbind(colnames(lf_duetP)
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, colnames(lf_foldxP)
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, colnames(lf_deepddgP)
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, colnames(lf_dynamut2P)
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, colnames(lf_consurfP)
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, colnames(lf_snap2P)
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, colnames(lf_proveanP)
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)
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bar
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lf_df_stabP = rbind((lf_duetP)
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, (lf_foldxP)
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, (lf_deepddgP)
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, (lf_dynamut2P))
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lf_df_consP = rbind((lf_consurfP)
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, (lf_snap2P)
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, (lf_proveanP))
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table(lf_df_stabP$param_type)
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# VERY USEFUL for seeing numbers for param types
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table(lf_df_stabP$param_type,lf_df_stabP$outcome)
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table(lf_df_consP$param_type,lf_df_consP$outcome)
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#==============
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# Plot:BP
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#==============
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stability_suffix <- paste0(delta_symbol, delta_symbol, "G")
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# lf_bp(lf_df_stabP, p_title = paste0("Stability",stability_suffix)
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# , violin_quantiles = c(0.5))
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# lf_bp(lf_df_consP, p_title = "Evolutionary Conservation"
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# , violin_quantiles = c(0.5))
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lf_bp2(lf_df_stabP, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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lf_bp2(lf_df_consP, p_title = "Evolutionary Conservation"
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, violin_quantiles = c(0.5), monochrome = F)
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#HMMM: Bollocks!
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lf_bp2(lf_commonP, p_title = paste0("Residue level properties")
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, violin_quantiles = c(0.5)
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, monochrome = T) # doesn't plot stat bars
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lf_bp(lf_commonP, p_title = paste0("Residue level properties")
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, violin_quantiles = c(0.5)) #plots stat bars but incorrect result
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lf_unpaired_stats(lf_duet)
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wilcox.test(wf_duet$`Lig Dist(Å)`[wf_duet$mutation_info_labels=="R"]
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, wf_duet$`Lig Dist(Å)`[wf_duet$mutation_info_labels=="S"])
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wilcox.test(wf_duet$ASA[wf_duet$mutation_info_labels=="R"]
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, wf_duet$ASA[wf_duet$mutation_info_labels=="S"])
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# 1: variable
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# 9: conserved
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# CHECK THESE
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foo = merged_df3[c("dst_mode", "mutation_info_labels", "consurf_colour_rev"
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, "consurf_scaled"
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, "consurf_score"
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, "consurf_outcome"
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, "snap2_score"
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, "snap2_scaled"
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, "snap2_outcome"
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, "provean_score"
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, "provean_scaled"
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, "provean_outcome")]
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################
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# Affinity
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################
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# ligand
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lf_mcsm_lig$outcome = lf_mcsm_lig$ligand_outcome
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lf_mcsm_lig$ligand_outcome = NULL
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colnames(lf_mcsm_lig)
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table(lf_mcsm_lig$param_type)
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lf_mcsm_lig$outcome = lf_mcsm_lig$ligand_outcome
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lf_mcsm_ligP = lf_mcsm_lig[!lf_mcsm_lig$param_type%in%c(static_colsP, "outcome"),]
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#lf_mcsm_ligP$param_type = levels(droplevels(lf_mcsm_ligP))
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table(lf_mcsm_ligP$param_type)
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lf_mcsm_ligP$ligand_outcome = NULL
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colnames(lf_mcsm_ligP)
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if (tolower(gene)%in%geneL_na){
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lf_mcsm_na$outcome = lf_mcsm_na$mcsm_na_outcome
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#lf_mcsm_na$mcsm_na_outcome = NULL
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lf_mcsm_naP = lf_mcsm_na[!lf_mcsm_na$param_type%in%c(static_colsP, "outcome"),]
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#lf_mcsm_naP$param_type = levels(droplevels(lf_mcsm_naP))
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table(lf_mcsm_naP$param_type)
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lf_mcsm_naP$mcsm_na_outcome = NULL
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colnames(lf_mcsm_naP)
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}
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if (tolower(gene)%in%geneL_ppi2){
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lf_mcsm_ppi2$outcome = lf_mcsm_ppi2$mcsm_ppi2_outcome
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colnames(lf_mcsm_ppi2)
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#lf_mcsm_ppi2$mcsm_ppi2_outcome = NULL
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lf_mcsm_ppi2P = lf_mcsm_ppi2[!lf_mcsm_ppi2$param_type%in%c(static_colsP, "outcome"),]
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#lf_mcsm_ppi2P$param_type = levels(droplevels(lf_mcsm_ppi2P))
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table(lf_mcsm_ppi2P$param_type)
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lf_mcsm_ppi2P$mcsm_ppi2_outcome = NULL
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colnames(lf_mcsm_ppi2P)
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}
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bar = rbind(colnames(lf_mcsm_ligP)
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#, colnames(lf_mcsm_naP)
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, colnames(lf_mcsm_ppi2P))
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bar
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lf_df_affP = rbind((lf_mcsm_ligP)
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, (lf_mcsm_ppi2P))
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lf_bp(lf_df_affP, p_title = paste0("Affinity changes")
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, violin_quantiles = c(0.5))
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#, monochrome = T) # doesn't plot stat bars
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wilcox.test(wf_mcsm_lig$ASA[wf_mcsm_lig$mutation_info_labels=="R"]
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, wf_mcsm_lig$ASA[wf_mcsm_lig$mutation_info_labels=="S"])
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wilcox.test(wf_mcsm_ppi2$ASA[wf_mcsm_ppi2$mutation_info_labels=="R"]
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, wf_mcsm_ppi2$ASA[wf_mcsm_ppi2$mutation_info_labels=="S"])
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#===============================
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p1 = lf_bp2(lf_df_stabP, p_title = paste0("Stability",stability_suffix)
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, violin_quantiles = c(0.5), monochrome = F)
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p2 = lf_bp2(lf_df_consP, p_title = "Evolutionary Conservation"
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, violin_quantiles = c(0.5), monochrome = F)
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p3 = lf_bp2(lf_df_affP, p_title = paste0("Affinity changes")
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, violin_quantiles = c(0.5), monochrome = F)
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cowplot::plot_grid(p1,cowplot::plot_grid(p2, p3), nrow=2)
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