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This commit is contained in:
Tanushree Tunstall 2020-09-18 18:07:48 +01:00
parent 093ae0d832
commit 771995d1ab
4 changed files with 33 additions and 12 deletions
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8
scripts/plotting/basic_barplots_LIG.R
View file

@ -78,7 +78,7 @@ theme_set(theme_grey())
# start plot 1
#--------------
g = ggplot(df, aes(x = ligand_outcome))
outPlot = g + geom_bar(aes(fill = ligand_outcome)
OutPlot_lig_count = g + geom_bar(aes(fill = ligand_outcome)
, show.legend = TRUE) +
geom_label(stat = "count"
, aes(label = ..count..)
@ -100,7 +100,7 @@ outPlot = g + geom_bar(aes(fill = ligand_outcome)
scale_fill_discrete(name = "Ligand Outcome"
, labels = c("Destabilising", "Stabilising"))
print(outPlot)
print(OutPlot_lig_count)
dev.off()
table(df$ligand_outcome)
@ -166,7 +166,7 @@ my_als = 22 # axis label size
my_x = sort(unique(snpsBYpos_df$snpsBYpos))
g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
outPlot_pos = g + geom_bar(aes (alpha = 0.5)
OutPlot_lig_pos_count = g + geom_bar(aes (alpha = 0.5)
, show.legend = FALSE) +
scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
#scale_x_continuous(breaks = my_x) +
@ -185,7 +185,7 @@ outPlot_pos = g + geom_bar(aes (alpha = 0.5)
labs(x = "Number of SNPs"
, y = "Number of Sites")
print(outPlot_pos)
print(OutPlot_lig_pos_count)
dev.off()
########################################################################
# end of lig barplots

12
scripts/plotting/basic_barplots_PS.R
View file

@ -64,7 +64,6 @@ str(df)
# Plot 1:Count of stabilising and destabilsing muts
#****************
#svg("basic_barplots_PS.svg")
svg(plot_basic_bp_duet)
print(paste0("plot1 filename:", basic_bp_duet))
@ -77,7 +76,7 @@ theme_set(theme_grey())
# start plot 1
#--------------
g = ggplot(df, aes(x = duet_outcome))
outPlot = g + geom_bar(aes(fill = duet_outcome)
OutPlot_count = g + geom_bar(aes(fill = duet_outcome)
, show.legend = TRUE) +
geom_label(stat = "count"
, aes(label = ..count..)
@ -99,7 +98,7 @@ outPlot = g + geom_bar(aes(fill = duet_outcome)
scale_fill_discrete(name = "DUET Outcome"
, labels = c("Destabilising", "Stabilising"))
print(outPlot)
print(OutPlot_count)
dev.off()
table(df$duet_outcome)
@ -153,7 +152,7 @@ foo = select(df, mutationinformation
#--------------
# start plot 2
#--------------
#svg("position_count_PS.svg")
svg(plot_pos_count_duet)
print(paste0("plot filename:", plot_pos_count_duet))
@ -165,7 +164,7 @@ my_als = 22 # axis label size
my_x = sort(unique(snpsBYpos_df$snpsBYpos))
g = ggplot(snpsBYpos_df, aes(x = snpsBYpos))
outPlot_pos = g + geom_bar(aes (alpha = 0.5)
OutPlot_pos_count = g + geom_bar(aes (alpha = 0.5)
, show.legend = FALSE) +
scale_x_continuous(breaks = unique(snpsBYpos_df$snpsBYpos)) +
#scale_x_continuous(breaks = my_x) +
@ -184,9 +183,8 @@ outPlot_pos = g + geom_bar(aes (alpha = 0.5)
labs(x = "Number of SNPs"
, y = "Number of Sites")
print(outPlot_pos)
print(OutPlot_pos_count)
dev.off()
########################################################################
# end of Ligand barplots
########################################################################

3
scripts/plotting/logo_combined.R
View file

@ -222,7 +222,8 @@ my_df_snp$log10or = log10(my_df_snp$or_mychisq)
logo_data = my_df_snp[, c("position", "mutant_type", "or_mychisq", "log10or")]
logo_data_or = my_df_snp[, c("position", "mutant_type", "or_mychisq")]
wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
#wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = 0.0)
wide_df_or <- logo_data_or %>% spread(position, or_mychisq, fill = NA)
wide_df_or = as.matrix(wide_df_or)
rownames(wide_df_or) = wide_df_or[,1]

22
scripts/plotting/other_plots.R
View file

@ -21,6 +21,10 @@ source("other_plots_data.R")
dr_other_combined = "dr_other_muts.svg"
plot_dr_other_combined = paste0(plotdir,"/", dr_other_combined)
dr_other_combined_labelled = "dr_other_muts_labelled.svg"
plot_dr_other_combined_labelled = paste0(plotdir,"/", dr_other_combined_labelled)
dr_other_foldx = "dr_other_muts_foldx.svg"
plot_dr_other_foldx = paste0(plotdir,"/", dr_other_foldx)
@ -214,6 +218,8 @@ svg(plot_dr_other_combined, width = 24, height = 12)
# first combine fold and lig plots (2 and 3)
c1 = cowplot::plot_grid(p2, p3
, labels = c("(b)", "(c)")
, label_size = 25
, nrow = 1
, rel_widths = c(1/6, 5/6))
c1
@ -223,6 +229,22 @@ OutPlot = cowplot::plot_grid(p1, c1
print(OutPlot)
dev.off()
#==========================================
# labelled
cat("Output plot:", plot_dr_other_combined_labelled)
svg(plot_dr_other_combined_labelled, width = 24, height = 12)
plot_dr_other_combined_labelled
Outplot_labelled = cowplot::plot_grid(p1, c1
, nrow = 2
, labels = c("(a)", "", "")
, label_size = 25)
print(Outplot_labelled)
dev.off()
#---------
# plot 3: legend
#---------