96 lines
3.1 KiB
R
96 lines
3.1 KiB
R
setwd("/home/tanu/git/LSHTM_analysis/scripts/plotting")
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source("combining_dfs_plotting.R")
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table(merged_df3$mutation_info)
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# assign foldx
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#ddg<0 = "Stabilising" (-ve)
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table(merged_df3$ddg < 0)
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merged_df3$foldx_outcome = ifelse(merged_df3$ddg < 0, "Stabilising", "Destabilising")
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#===========
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# PS data
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#===========
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dr_muts = merged_df3[merged_df3$mutation_info == "dr_mutations_pyrazinamide",]
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other_muts = merged_df3[merged_df3$mutation_info == "other_mutations_pyrazinamide",]
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par(mfrow = c(1,1))
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par(mfrow = c(2,6))
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# mcsm duet
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boxplot(dr_muts$duet_scaled, other_muts$duet_scaled, main = "DUET"
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#, col = factor(merged_df3$duet_outcome)
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)
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wilcox.test(dr_muts$duet_scaled, other_muts$duet_scaled, paired = F)
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# foldx ddg
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boxplot(dr_muts$ddg, other_muts$ddg, main = "Foldx")
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wilcox.test(dr_muts$ddg, other_muts$ddg, paired = F)
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# rd
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boxplot(dr_muts$rd_values, other_muts$rd_values, main = "RD")
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wilcox.test(dr_muts$rd_values, other_muts$rd_values)
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# kd
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boxplot(dr_muts$kd_values, other_muts$kd_values, main = "KD")
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wilcox.test(dr_muts$kd_values, other_muts$kd_values)
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# asa
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boxplot(dr_muts$asa, other_muts$asa, main = "ASA")
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wilcox.test(dr_muts$asa, other_muts$asa)
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# rsa
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boxplot(dr_muts$rsa, other_muts$rsa, main = "RSA")
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wilcox.test(dr_muts$rsa, other_muts$rsa)
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#===================================================================
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#==========
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# LIG data
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#==========
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dr_muts_lig = merged_df3_lig[merged_df3_lig$mutation_info == "dr_mutations_pyrazinamide",]
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other_muts_lig = merged_df3_lig[merged_df3_lig$mutation_info == "other_mutations_pyrazinamide",]
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# mcsm ligand affinity
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boxplot(dr_muts_lig$duet_scaled, other_muts_lig$duet_scaled, main = "Ligand affinity")
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wilcox.test(dr_muts_lig$duet_scaled, other_muts_lig$duet_scaled, paired = F)
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# rd
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boxplot(dr_muts_lig$rd_values, other_muts_lig$rd_values, main = "RD")
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wilcox.test(dr_muts_lig$rd_values, other_muts_lig$rd_values)
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# kd
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boxplot(dr_muts_lig$kd_values, other_muts_lig$kd_values, main = "KD")
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wilcox.test(dr_muts_lig$kd_values, other_muts_lig$kd_values)
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# asa
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boxplot(dr_muts_lig$asa, other_muts_lig$asa, main = "ASA")
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wilcox.test(dr_muts_lig$asa, other_muts_lig$asa)
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# rsa
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boxplot(dr_muts_lig$rsa, other_muts_lig$rsa, main = "RSA")
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wilcox.test(dr_muts_lig$rsa, other_muts_lig$rsa)
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# checking agreement b/w mcsm and foldx
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cols_to_select = c("mutationinformation"
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, "mutation_info"
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, "duet_scaled"
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, "ddg"
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, "duet_outcome"
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, "foldx_outcome")
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merged_df3_short = select(merged_df3, cols_to_select)
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mcsm_foldx = merged_df3_short[which(merged_df3_short$duet_outcome != merged_df3_short$foldx_outcome),]
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mcsm_foldx$sign_comp = ifelse(sign(mcsm_foldx$duet_scaled)==sign(mcsm_foldx$ddg), "PASS", "FAIL")
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table(mcsm_foldx$sign_comp)
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# another way of checking
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merged_df3$sign_comp = ifelse(sign(merged_df3$duet_scaled)==sign(merged_df3$ddg), "PASS", "FAIL")
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table(merged_df3$sign_comp)
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disagreement = table(merged_df3$sign_comp)[2]/nrow(merged_df3)*100
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agreement = 100 - disagreement
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cat("There is", agreement, "% between mcsm and foldx predictions")
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