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added delta symbol to plotting_data.R and pretty labels for dr_other_muts figure

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Tanushree Tunstall 2020-09-11 14:40:37 +01:00
parent ecbc7541e9
commit 8d9ede186c
3 changed files with 108 additions and 83 deletions
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161
scripts/plotting/other_plots.R
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@ -32,12 +32,13 @@ plot_point_legend = paste0(plotdir,"/", point_legend)
#my_comparisons <- list( c(dr_muts_col, other_muts_col) ) #my_comparisons <- list( c(dr_muts_col, other_muts_col) )
my_comparisons <- list( c("DM", "OM") ) my_comparisons <- list( c("DM", "OM") )
my_ats = 22# axis text size
my_ats = 15# axis text size
my_als = 20 # axis label size my_als = 20 # axis label size
my_fls = 20 # facet label size my_fls = 20 # facet label size
my_pts = 22 # plot title size my_pts = 22 # plot title size
##########################################################################
#=========== #===========
# Plot1: PS # Plot1: PS
#=========== #===========
@ -65,7 +66,8 @@ p1 = ggplot(df_lf_ps, aes(x = mutation_info
, vjust = 0) , vjust = 0)
, axis.title.x = element_text(size = my_ats) , axis.title.x = element_text(size = my_ats)
, axis.title.y = element_text(size = my_ats) , axis.title.y = element_text(size = my_ats)
, plot.title = element_text(size = my_pts , hjust = 0.5) , plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
, strip.background = element_rect(fill = "khaki2")
, strip.text.x = element_text(size = my_fls, colour = "black") , strip.text.x = element_text(size = my_fls, colour = "black")
, legend.title = element_text(color = "black", size = my_als) , legend.title = element_text(color = "black", size = my_als)
, legend.text = element_text(size = my_ats) , legend.text = element_text(size = my_ats)
@ -79,17 +81,65 @@ p1 = ggplot(df_lf_ps, aes(x = mutation_info
#, label = "p.format") #, label = "p.format")
, label = "p.signif") , label = "p.signif")
p1 p1
#===============================================================
#=========== ##########################################################################
# Plot 2: LIG #=================
#=========== # Plot 2: Foldx
#=================
my_stat_foldx = compare_means(param_value~mutation_info, group.by = "param_type"
, data = df_lf_foldx, paired = FALSE, p.adjust.method = "BH")
y_value = "param_value"
p2 = ggplot(df_lf_foldx, aes(x = mutation_info
, y = eval(parse(text=y_value)) )) +
facet_wrap(~ param_type
, nrow = 1
, scales = "free_y") +
geom_boxplot(fill = "white", outlier.colour = NA
#, position = position_dodge(width = 0.2)
, width = 0.5) +
geom_point(position = position_jitterdodge(dodge.width=0.01)
, alpha = 0.5
, show.legend = FALSE
, aes(colour = factor(foldx_outcome))) +
theme(axis.text.x = element_text(size = my_ats)
, axis.text.y = element_text(size = my_ats
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_text(size = my_ats)
, plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
, strip.background = element_rect(fill = "palegreen1")
, strip.text.x = element_text(size = my_fls, colour = "black")
, legend.title = element_text(color = "black", size = my_als)
, legend.text = element_text(size = my_ats)
#, legend.title = element_blank()
, legend.direction = "vertical") +
labs(title = "Foldx"
, x = ""
, y = "") +
stat_compare_means(comparisons = my_comparisons
, method = "wilcox.test"
, paired = FALSE
#, label = "p.format")
, label = "p.signif")
p2
##########################################################################
#==============
# Plot 3: LIG
#==============
my_stat_lig = compare_means(param_value~mutation_info, group.by = "param_type" my_stat_lig = compare_means(param_value~mutation_info, group.by = "param_type"
, data = df_lf_lig, paired = FALSE, p.adjust.method = "BH") , data = df_lf_lig, paired = FALSE, p.adjust.method = "BH")
y_value = "param_value" y_value = "param_value"
p2 = ggplot(df_lf_lig, aes(x = mutation_info p3 = ggplot(df_lf_lig, aes(x = mutation_info
, y = eval(parse(text=y_value)) )) + , y = eval(parse(text=y_value)) )) +
facet_wrap(~ param_type facet_wrap(~ param_type
, nrow = 1 , nrow = 1
@ -108,7 +158,8 @@ p2 = ggplot(df_lf_lig, aes(x = mutation_info
, vjust = 0) , vjust = 0)
, axis.title.x = element_text(size = my_ats) , axis.title.x = element_text(size = my_ats)
, axis.title.y = element_text(size = my_ats) , axis.title.y = element_text(size = my_ats)
, plot.title = element_text(size = my_pts , hjust = 0.5) , plot.title = element_text(size = my_pts , hjust = 0.5, colour = "black", face = "bold")
, strip.background = element_rect(fill = "thistle3")
, strip.text.x = element_text(size = my_fls, colour = "black") , strip.text.x = element_text(size = my_fls, colour = "black")
, legend.title = element_text(color = "black", size = my_als) , legend.title = element_text(color = "black", size = my_als)
, legend.text = element_text(size = my_ats) , legend.text = element_text(size = my_ats)
@ -122,58 +173,12 @@ p2 = ggplot(df_lf_lig, aes(x = mutation_info
#, label = "p.format") #, label = "p.format")
, label = "p.signif") , label = "p.signif")
p2
#====================================================================
#===========
# Plot 3: Foldx
#===========
my_stat_foldx = compare_means(param_value~mutation_info, group.by = "param_type"
, data = df_lf_foldx, paired = FALSE, p.adjust.method = "BH")
y_value = "param_value"
p3 = ggplot(df_lf_foldx, aes(x = mutation_info
, y = eval(parse(text=y_value)) )) +
facet_wrap(~ param_type
, nrow = 1
, scales = "free_y") +
geom_boxplot(fill = "white", outlier.colour = NA
#, position = position_dodge(width = 0.2)
, width = 0.5) +
geom_point(position = position_jitterdodge(dodge.width=0.01)
, alpha = 0.5
, show.legend = FALSE
, aes(colour = factor(foldx_outcome))) +
theme(axis.text.x = element_text(size = my_ats)
, axis.text.y = element_text(size = my_ats
, angle = 0
, hjust = 1
, vjust = 0)
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_text(size = my_ats)
, plot.title = element_text(size = my_pts , hjust = 0.5)
, strip.text.x = element_text(size = my_fls, colour = "black")
#, legend.title = element_text(color = "black", size = my_als)
, legend.text = element_text(size = my_ats)
, legend.direction = "vertical"
, legend.title = element_blank()) +
labs(title = ""
, x = ""
, y = "") +
stat_compare_means(comparisons = my_comparisons
, method = "wilcox.test"
, paired = FALSE
#, label = "p.format")
, label = "p.signif")
p3 p3
#==================================================================== ##########################################################################
#=========== #===========
# legend # legend
#=========== #===========
legend = ggplot(df_lf_foldx, aes(x = mutation_info legend = ggplot(df_lf_foldx, aes(x = mutation_info
, y = eval(parse(text=y_value)) )) + , y = eval(parse(text=y_value)) )) +
facet_wrap(~ param_type facet_wrap(~ param_type
@ -186,12 +191,15 @@ legend = ggplot(df_lf_foldx, aes(x = mutation_info
, aes(colour = factor(foldx_outcome))) + , aes(colour = factor(foldx_outcome))) +
theme(legend.text = element_text(size = 25) theme(legend.text = element_text(size = 25)
, legend.direction = "vertical" , legend.direction = "vertical"
, legend.title = element_blank())+ , legend.title = element_blank()
#, axis.text.y = element_text(size = 30, colour = "black", angle = 90)
#, axis.text.x = element_text(size = 30, colour = "black", angle = 0)
#, strip.background = element_rect(fill="orange")
) +
guides(color = guide_legend(override.aes = list(size = 6))) guides(color = guide_legend(override.aes = list(size = 6)))
legend legend
##########################################################################
#=========================== #===========================
# combine # combine
#=========================== #===========================
@ -202,24 +210,19 @@ cat("Output plot:",plot_dr_other_combined)
svg(plot_dr_other_combined, width = 24, height = 12) svg(plot_dr_other_combined, width = 24, height = 12)
#theme_set(theme_gray()) # to preserve default theme #theme_set(theme_gray()) # to preserve default theme
OutPlot = cowplot::plot_grid(p1, p2
, nrow = 2
, align = "hv" # first combine fold and lig plots (2 and 3)
, axis = "b" c1 = cowplot::plot_grid(p2, p3
, labels = c("", "", "") , nrow = 1
, label_size = my_als) , rel_widths = c(1/6, 5/6))
c1
OutPlot = cowplot::plot_grid(p1, c1
, nrow = 2)
print(OutPlot) print(OutPlot)
dev.off() dev.off()
#---------
# plot 2
#---------
svg(plot_dr_other_foldx , width = 6, height = 7)
OutPlot2 = p3
print(OutPlot2)
dev.off()
#--------- #---------
# plot 3: legend # plot 3: legend
#--------- #---------
@ -227,3 +230,13 @@ svg(plot_point_legend, width = 6, height = 7)
OutPlot3 = legend OutPlot3 = legend
print(OutPlot3) print(OutPlot3)
dev.off() dev.off()

26
scripts/plotting/other_plots_data.R
View file

@ -110,14 +110,12 @@ df_lig = merged_df3_lig
# name tidying # name tidying
df_lig$mutation_info = as.factor(df_lig$mutation_info) df_lig$mutation_info = as.factor(df_lig$mutation_info)
df_lig$duet_outcome = as.factor(df_lig$duet_outcome) df_lig$duet_outcome = as.factor(df_lig$duet_outcome)
df_lig$ligand_outcome = as.factor(df_lig$ligand_outcome) #df_lig$ligand_outcome = as.factor(df_lig$ligand_outcome)
# check # check
table(df_lig$mutation_info) table(df_lig$mutation_info)
#======================================================================== #========================================================================
#=========== #===========
# Data: ps # Data: ps
#=========== #===========
@ -155,8 +153,16 @@ str(df_lf_ps)
# assign pretty labels: param_type # assign pretty labels: param_type
levels(df_lf_ps$param_type); table(df_lf_ps$param_type) levels(df_lf_ps$param_type); table(df_lf_ps$param_type)
levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="duet_scaled"] <- "DUET" ligand_dist_colname = paste0("Distance to ligand (", angstroms_symbol, ")")
levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="ligand_distance"] <- "Ligand Distance" ligand_dist_colname
duet_stability_name = paste0(delta_symbol, delta_symbol, "G")
duet_stability_name
#levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="duet_scaled"] <- "Stability"
levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="duet_scaled"] <- duet_stability_name
#levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="ligand_distance"] <- "Ligand Distance"
levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="ligand_distance"] <- ligand_dist_colname
levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="asa"] <- "ASA" levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="asa"] <- "ASA"
levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="rsa"] <- "RSA" levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="rsa"] <- "RSA"
levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="rd_values"] <- "RD" levels(df_lf_ps$param_type)[levels(df_lf_ps$param_type)=="rd_values"] <- "RD"
@ -183,7 +189,7 @@ cols_to_select_lig = c("mutationinformation", "mutation", "position", "mutation_
, "ligand_outcome" , "ligand_outcome"
, "affinity_scaled" , "affinity_scaled"
, "ligand_distance" #, "ligand_distance"
, "asa" , "asa"
, "rsa" , "rsa"
, "rd_values" , "rd_values"
@ -210,7 +216,7 @@ if (nrow(df_lf_lig) == expected_rows_lf_lig){
levels(df_lf_lig$param_type); table(df_lf_lig$param_type) levels(df_lf_lig$param_type); table(df_lf_lig$param_type)
levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="affinity_scaled"] <- "Ligand Affinity" levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="affinity_scaled"] <- "Ligand Affinity"
levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="ligand_distance"] <- "Ligand Distance" #levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="ligand_distance"] <- "Ligand Distance"
levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="asa"] <- "ASA" levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="asa"] <- "ASA"
levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="rsa"] <- "RSA" levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="rsa"] <- "RSA"
levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="rd_values"] <- "RD" levels(df_lf_lig$param_type)[levels(df_lf_lig$param_type)=="rd_values"] <- "RD"
@ -260,10 +266,14 @@ if (nrow(df_lf_foldx) == expected_rows_lf_foldx){
exit() exit()
} }
foldx_stability_name = paste0(delta_symbol, delta_symbol, "G")
foldx_stability_name
# assign pretty labels: param type # assign pretty labels: param type
levels(df_lf_foldx$param_type); table(df_lf_foldx$param_type) levels(df_lf_foldx$param_type); table(df_lf_foldx$param_type)
levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="foldx_scaled"] <- "Foldx" #levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="foldx_scaled"] <- "Stability"
levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="foldx_scaled"] <- foldx_stability_name
#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="ligand_distance"] <- "Ligand Distance" #levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="ligand_distance"] <- "Ligand Distance"
#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="asa"] <- "ASA" #levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="asa"] <- "ASA"
#levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="rsa"] <- "RSA" #levels(df_lf_foldx$param_type)[levels(df_lf_foldx$param_type)=="rsa"] <- "RSA"

2
scripts/plotting/plotting_data.R
View file

@ -97,6 +97,8 @@ my_df_u_lig = my_df_u[my_df_u$ligand_distance <10,]
angstroms_symbol = "\u212b" angstroms_symbol = "\u212b"
cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10", angstroms_symbol, " of the ligand\n")) cat(paste0("There are ", nrow(my_df_u_lig), " sites lying within 10", angstroms_symbol, " of the ligand\n"))
delta_symbol = "\u0394"; delta_symbol
######################################################################## ########################################################################
# end of data extraction and cleaning for plots # # end of data extraction and cleaning for plots #
######################################################################## ########################################################################