diff --git a/config/alr.R b/config/alr.R index b007c5b..38ca6cc 100644 --- a/config/alr.R +++ b/config/alr.R @@ -1,2 +1,33 @@ gene = "alr" drug = "cycloserine" + +aa_plip = c(66, 70, 112, 196, 237, 252, 254, 255, 295, 314, 343) +aa_ligplus = c(66, 64, 70, 112, 196, 236, 237, 252, 253, 254, 255, 388 ) +#active_aa_pos = c(66, 64, 70, 112, 196, 236, 237, 252, 253, 254, 255, 295, 314, 343, 388) +active_aa_pos = sort(unique(c(aa_plip, aa_ligplus))) + +#aa_plip = c(66 = "hbond" +#, 70 = "hbond" +#, 112 = "hydrophobic" +#, 196 = "hbond" +#, 237 = "hbond" +#, 252 = "hbond" +#, 254 = "hbond" +#, 255 = "hbond" +#, 295 = "hbond" +#, 314 = "hbond" +#, 343 = "hbond") + +#aa_ligplus = c(66 = "hbond" +#, 64 = "hydrophobic" +#, 70 = "hydrophobic" +#, 112 = "hydrophobic" +#, 196 = "hbond" +#, 236 = "hydrophobic" +#, 237 = "hbond" +#, 252 = "hydrophobic" +#, 253 = "hydrophobic" +#, 254 = "hbond" +#, 255 = "hbond" +#, 388 = "hydrophobic" +#) diff --git a/config/embb.R b/config/embb.R index a74ce66..0009583 100644 --- a/config/embb.R +++ b/config/embb.R @@ -1,2 +1,7 @@ gene = "embB" drug = "ethambutol" + +aa_plip = c(299, 302, 303, 327, 594, 988, 1028 ) +aa_ligplus = c(299, 302, 303, 306, 334, 594, 988, 1028) +#active_aa_pos = c(299, 302, 303, 306, 327, 334, 594, 988, 1028 ) +active_aa_pos = sort(unique(c(aa_plip, aa_ligplus))) diff --git a/config/gid.R b/config/gid.R index 983ed71..a2f9981 100644 --- a/config/gid.R +++ b/config/gid.R @@ -3,7 +3,13 @@ drug = "streptomycin" rna_bind_aa_pos = c(96, 97, 118, 163) binding_aa_pos = c(48, 51, 137, 200) -active_aa_pos = sort(unique(c(rna_bind_aa_pos, binding_aa_pos))) +aa_plip = c(118, 220, 223) +aa_ligplus = c(118, 220, 223) + +active_aa_pos = sort(unique(c(rna_bind_aa_pos +, binding_aa_pos +, aa_plip +, aa_ligplus))) #rna_site = G518 cat("\nNo. of active site residues for gene" @@ -18,4 +24,4 @@ cat("\n===================================================" , "\nRNA binding residues:" , rna_bind_aa_pos , "\nBinding site residues:" - , binding_aa_pos) \ No newline at end of file + , binding_aa_pos) diff --git a/config/katg.R b/config/katg.R index f8603b0..cf73f39 100644 --- a/config/katg.R +++ b/config/katg.R @@ -1,2 +1,6 @@ gene = "katG" drug = "isoniazid" + +aa_plip = c(104, 229, 230) +aa_ligplus = c(107, 108, 137, 229, 230) +active_aa_pos = sort(unique(c(aa_plip, aa_ligplus))) diff --git a/config/pnca.R b/config/pnca.R index 5a9a902..349278e 100644 --- a/config/pnca.R +++ b/config/pnca.R @@ -7,6 +7,10 @@ drug = "pyrazinamide" #Substrate binding --> teal and blue #H-bond --> green #==================================== +#aa_plip = c(49, 51, 57, 71, 96 , 133, 134, 138) +#aa_ligplus = c(8, 13 , 49 , 133, 134 , 138, 137) +#active_aa_pos = sort(unique(c(aa_plip, aa_ligplus))) + metal_aa_pos = c(49, 51, 57, 71) catalytic_aa_pos = c(8, 96, 138) substrate_aa_pos = c(13, 68, 103, 137) @@ -33,4 +37,4 @@ cat("\n===================================================" , "\nSubstrate binding residues:" , substrate_aa_pos , "\nH-bonding residues:" - , hbond_aa_pos) \ No newline at end of file + , hbond_aa_pos) diff --git a/config/rpob.R b/config/rpob.R index 76ab98e..5a8db53 100644 --- a/config/rpob.R +++ b/config/rpob.R @@ -1,2 +1,6 @@ gene = "rpoB" drug = "rifampicin" + +aa_plip = c(429, 432, 491, 487) +aa_plip_5uhc = c(430, 452, 483, 491, 432, 433, 448, 450, 459, 487) +active_aa_pos = sort(unique(c(aa_plip, aa_plip_5uhc))) diff --git a/scripts/plotting/consurf_plot.R b/scripts/plotting/consurf_plot.R index 0d77bd2..916aee3 100644 --- a/scripts/plotting/consurf_plot.R +++ b/scripts/plotting/consurf_plot.R @@ -1,4 +1,4 @@ -myColors1 = c("0" = "yellow2" +consurf_palette1 = c("0" = "yellow2" , "1" = "cyan1" , "2" = "steelblue2" , "3" = "cadetblue2" @@ -9,8 +9,7 @@ myColors1 = c("0" = "yellow2" , "8" = "maroon" , "9" = "violetred2") - -myColors2 = c("0" = "yellow2" +consurf_palette2 = c("0" = "yellow2" , "1" = "forestgreen" , "2" = "seagreen3" , "3" = "palegreen1" @@ -22,10 +21,21 @@ myColors2 = c("0" = "yellow2" , "9" = "darkorchid4") -#myColors <- colorRampPalette(c("cyan", "violetred4"))(9) +#myCOL <- colorRampPalette(c("yellow2", "palegreen1", "darkorchid4"))(10) +#plot(1:100, col = myCOL, pch = 19, cex = 2) #myColors <- scale_color_brewer(palette = "Cyan-Magenta") -breaks <- levels(as.factor(mtcars$cyl)) -colours <- ifelse(breaks == 4, "red", "blue") + +consurf_cols = consurf_palette1 +consurf_cols = consurf_palette2 +#consurf_cols = myCOL +consurf_col_labs = c("Insufficient Data" + , "Variable" + , "2", "3", "4", "5" + , "6", "7", "8", "Conserved") + + +#breaks <- levels(as.factor(mtcars$cyl)) +#colours <- ifelse(breaks == 4, "red", "blue") aa_position_colname = "position" length(unique(merged_df3[[aa_position_colname]])) @@ -42,15 +52,6 @@ bar[['lab_bg']] = ifelse(bar[[aa_position_colname]]%in%rna_bind_aa_pos head(bar[[aa_position_colname]]) head(bar[['lab_bg']]) -#bar2 = as.data.frame(cbind(bar[[aa_position]], bar[['lab_bg']]) ) - - - - -#geom_tile(aes(,-0.8, width = 0.95, height = 0.85) -# , fill = df$lab_bg) + -#geom_tile(aes(,-1.2, width = 0.95, height = -0.2) -# , fill = df$lab_bg2) + my_xlim = length(unique(bar$position)); my_xlim ymin = min(bar$consurf_score) @@ -64,8 +65,9 @@ g = ggplot(bar, aes(x = factor(position) , ylim = c(ymin, ymax) , clip = "off") + geom_point() + - #scale_colour_manual( values = myColors1) + - scale_colour_manual( values = myColors2) + + scale_colour_manual( values = consurf_cols + , labels = consurf_col_labs + ) + geom_errorbar(aes(ymin = consurf_ci_lower, ymax = consurf_ci_upper)) g0 = g + geom_tile(aes(,-2, width = 0.95, height = -0.2) @@ -93,11 +95,9 @@ g1 = g0 + theme( axis.text.x = element_text(size = 10 #, direction = "horizontal" )) + labs(title = "" - , x = "Position" - , y = "Consurf_score") + , x = "Wild-type position" + , y = "Consurf score") g1 - - ##########################################