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added hbond residues in config for all genes

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This commit is contained in:
Tanushree Tunstall 2022-02-09 15:59:18 +00:00
parent 7a14655ecb
commit 6ffb084546
9 changed files with 686 additions and 110 deletions
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23
scripts/Header_TT.R
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@ -193,6 +193,29 @@ map(paste0(func_path, source_files), source) # source all your R scripts!
# set plot script dir
plot_script_path = "~/git/LSHTM_analysis/scripts/plotting/"
####################################################
consurf_palette1 = c("0" = "yellow2"
, "1" = "cyan1"
, "2" = "steelblue2"
, "3" = "cadetblue2"
, "4" = "paleturquoise2"
, "5" = "thistle3"
, "6" = "thistle2"
, "7" = "plum2"
, "8" = "maroon"
, "9" = "violetred2")
consurf_palette2 = c("0" = "yellow2"
, "1" = "forestgreen"
, "2" = "seagreen3"
, "3" = "palegreen1"
, "4" = "darkseagreen2"
, "5" = "thistle3"
, "6" = "lightpink1"
, "7" = "orchid3"
, "8" = "orchid4"
, "9" = "darkorchid4")
##################################################
# Function name clashes with plyr and dplyr

2
scripts/plotting/barplots_subcolours_aa_PS.R
View file

@ -213,7 +213,7 @@ g = ggplot(df, aes(factor(position, ordered = T)))
# This is the key to generating the geom_tiles OUTside the plotting area on the x-axis!
OutPlot_aa_PS = g +
coord_cartesian(xlim = c(1, my_xlim)
#, ylim = c(0, 6)
#, ylim = c(0, 6)0.85
, ylim = c(0, max(snp_count))
, clip = "off") +
geom_bar(aes(fill = group), colour = "grey") +

199
scripts/plotting/consurf_plot.R
View file

@ -1,30 +1,3 @@
consurf_palette1 = c("0" = "yellow2"
, "1" = "cyan1"
, "2" = "steelblue2"
, "3" = "cadetblue2"
, "4" = "paleturquoise2"
, "5" = "thistle3"
, "6" = "thistle2"
, "7" = "plum2"
, "8" = "maroon"
, "9" = "violetred2")
consurf_palette2 = c("0" = "yellow2"
, "1" = "forestgreen"
, "2" = "seagreen3"
, "3" = "palegreen1"
, "4" = "darkseagreen2"
, "5" = "thistle3"
, "6" = "lightpink1"
, "7" = "orchid3"
, "8" = "orchid4"
, "9" = "darkorchid4")
#myCOL <- colorRampPalette(c("yellow2", "palegreen1", "darkorchid4"))(10)
#plot(1:100, col = myCOL, pch = 19, cex = 2)
#myColors <- scale_color_brewer(palette = "Cyan-Magenta")
consurf_cols = consurf_palette1
consurf_cols = consurf_palette2
#consurf_cols = myCOL
@ -42,17 +15,20 @@ length(unique(merged_df3[[aa_position_colname]]))
positionF <- levels(as.factor(merged_df3[[aa_position_colname]]))
length(positionF)
aa_pos_colours = ifelse(positionF%in%rna_bind_aa_pos, "purple"
, ifelse(positionF%in%binding_aa_pos, "orange", "black" ))
aa_pos_colours = ifelse(positionF%in%aa_pos_sry, "purple"
, ifelse(positionF%in%aa_pos_rna, "orange", "black" ))
bar = merged_df3
bar[['lab_bg']] = ifelse(bar[[aa_position_colname]]%in%rna_bind_aa_pos
aa_colour_colname = "lab_bg"
bar[[aa_colour_colname]] = ifelse(bar[[aa_position_colname]]%in%aa_pos_sry
, "purple"
, ifelse(bar[[aa_position_colname]]%in%binding_aa_pos
, ifelse(bar[[aa_position_colname]]%in%aa_pos_rna
, "orange", "white" ))
head(bar[[aa_position_colname]])
head(bar[['lab_bg']])
head(bar[[aa_colour_colname]])
my_xlim = length(unique(bar$position)); my_xlim
######################################################################
my_xlim = length(unique(bar[[aa_position_colname]])); my_xlim
ymin = min(bar$consurf_score)
ymax = max(bar$consurf_score)
@ -70,15 +46,38 @@ g = ggplot(bar, aes(x = factor(position)
) +
geom_errorbar(aes(ymin = consurf_ci_lower, ymax = consurf_ci_upper))
g0 = g + geom_tile(aes(,-2, width = 0.95, height = -0.2)
, fill = bar$lab_bg
, colour = "white")
g0
g1 = g0 + theme( axis.text.x = element_text(size = 10
# g0 = g + geom_tile(aes(,-2, width = 0.95, height = -0.2)
# #, fill = bar$lab_bg
# , fill = bar[[aa_colour_colname]]
# , colour = "white")
g0 = g +
geom_tile(aes(,-1.7, width = 0.95, height = 0.3)
, fill = bar$ligD_colours
, colour = "black")
# g0 = g +
# geom_tile(aes(,-1.9, width = 0.95, height = 0.2)
# , fill = bar[[aa_colour_colname4]]
# , colour = "white") +
# geom_tile(aes(,-2, width = 0.95, height = 0.3)
# , fill = bar[[aa_colour_colname3]]
# , colour = "white"
# )+
# geom_tile(aes(,-2.1, width = 0.95, height = 0.35)
# , fill = bar[[aa_colour_colname2]]
# , colour = "white"
# )+
# geom_tile(aes(,-2.2, width = 0.95, height = 0.45)
# , fill = bar[[aa_colour_colname1]]
# , colour = "white"
# )
g1 = g + theme( axis.text.x = element_text(size = 10
, angle = 90
, hjust = 1
, vjust = 0.4
, face = "bold"
#, colour = aa_pos_colours
)
, axis.text.y = element_text(size = 12
@ -92,12 +91,128 @@ g1 = g0 + theme( axis.text.x = element_text(size = 10
, panel.grid.minor = element_line(color = "black")) +
guides(colour = guide_legend(title = "Consurf"
, position = "top"
#, direction = "horizontal"
#, direction = "horizontal"
)) +
labs(title = ""
, x = "Wild-type position"
#, x = "Wild-type position"
, x = ""
, y = "Consurf score")
g1
##########################################
# add tile afterwards
g2 = g1 + geom_tile(aes(,-1.7, width = 0.95, height = 0.3)
, fill = bar$ligD_colours
, colour = "black")
g2
g3 = g2 +
geom_tile(aes(,-1.9, width = 0.95, height = 0.3)
, fill = bar[[aa_colour_colname4]]
, colour = "white") +
geom_tile(aes(,-2, width = 0.95, height = 0.3)
, fill = bar[[aa_colour_colname3]]
, colour = "white"
)+
geom_tile(aes(,-2.1, width = 0.95, height = 0.35)
, fill = bar[[aa_colour_colname2]]
, colour = "white"
)+
geom_tile(aes(,-2.2, width = 0.95, height = 0.35)
, fill = bar[[aa_colour_colname1]]
, colour = "white"
)
g3
#==============================================
#Multiple legends in a plot with geom_tile
#==============================================
# https://stackoverflow.com/questions/24822621/multiple-legends-in-a-plot-with-geom-tile
g_legend<-function(a.gplot){
tmp <- ggplot_gtable(ggplot_build(a.gplot))
leg <- which(sapply(tmp$grobs, function(x) x$name) == "guide-box")
legend <- tmp$grobs[[leg]]
legend
}
legend1 = g_legend(g1)
g2 = g1 + geom_tile(aes(,-1.7, width = 0.95, height = 0.3)
, fill = bar$ligD_colours
, colour = "black")
g2
legend2 = g_legend(g2)
grid.arrange(g1+theme(legend.position = 'none')
#, legend1
, legend2
, ncol = 2
, widths=c(4/6, 1/6))
###############################################################
###############################################################
lig_min = min(round(bar[[LigDist_colname]])); lig_min
lig_max = max(round(bar[[LigDist_colname]])); lig_max
lig_mean = round(mean(bar[[LigDist_colname]])); lig_mean
labels = seq(lig_min, lig_max, len = 5); labels
labelsD = round(labels, digits = 0); labelsD
g = ggplot(bar, aes( x = factor(.data[[aa_position_colname]])
, y = .data[[LigDist_colname]]))
g
# yayy
g1 = g + geom_tile(aes(fill = .data[[LigDist_colname]])
, colour = "white") +
#scale_fill_gradient(low = "green", high = "red")
scale_fill_gradient2(midpoint = lig_mean
, low = "green"
, mid = "yellow"
, high = "red"
, breaks = labels
#, n.breaks = 11
#, minor_breaks = c(2, 4, 6, 8, 10)
, limits = c(lig_min, lig_max)
, labels = labelsD
, name = "Ligand Distance")
g1
main_leg = g_legend(g2)
main_leg
ligD_leg = g_legend(g1)
grid.arrange(ligD_leg
, ncol = 2
, widths=c(4/6, 1/6))
grid.arrange(g2+theme(legend.position = 'none')
, main_leg
, ligD_leg
, ncol = 3
, widths=c(9/10, 0.5/10, 0.5/10))
##########################
g3 = g2 + theme(legend.position = 'none')
g3
g4 = g3 + geom_tile(aes(fill = .data[['consurf_score']])
, colour = "white")
g4 + geom_tile(scale_fill_gradient(consurf_palette2)
midpoint = lig_mean
, low = "green"
, mid = "yellow"
, high = "red"
, breaks = labels
#, n.breaks = 11
#, minor_breaks = c(2, 4, 6, 8, 10)
, limits = c(lig_min, lig_max)
, labels = labelsD
, name = "Ligand Distance")
g1