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added active site positions to all config.R

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This commit is contained in:
Tanushree Tunstall 2022-02-03 18:02:27 +00:00
parent 04cddbbf2b
commit 7a14655ecb
7 changed files with 78 additions and 24 deletions
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31
config/alr.R
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@ -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"
#)

5
config/embb.R
View file

@ -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)))

10
config/gid.R
View file

@ -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)
, binding_aa_pos)

4
config/katg.R
View file

@ -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)))

6
config/pnca.R
View file

@ -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)
, hbond_aa_pos)

4
config/rpob.R
View file

@ -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)))

42
scripts/plotting/consurf_plot.R
View file

@ -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
##########################################