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updated with two outputs: labelled and unlabelled

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This commit is contained in:
Tanushree Tunstall 2020-09-16 15:37:56 +01:00
parent 351e472e73
commit a5b03e53e8
1 changed files with 26 additions and 69 deletions
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95
scripts/plotting/lineage_dist_dm_om_combined_PS.R
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@ -16,6 +16,7 @@ getwd()
source("Header_TT.R") source("Header_TT.R")
library(ggridges) library(ggridges)
library(plyr)
source("combining_dfs_plotting.R") source("combining_dfs_plotting.R")
# PS combined: # PS combined:
# 1) merged_df2 # 1) merged_df2
@ -61,6 +62,9 @@ cat("cols imported:"
#======= #=======
lineage_dist_combined_dm_om = "lineage_dist_combined_dm_om_PS.svg" lineage_dist_combined_dm_om = "lineage_dist_combined_dm_om_PS.svg"
plot_lineage_dist_combined_dm_om = paste0(plotdir,"/", lineage_dist_combined_dm_om) plot_lineage_dist_combined_dm_om = paste0(plotdir,"/", lineage_dist_combined_dm_om)
lineage_dist_combined_dm_om_L = "lineage_dist_combined_dm_om_PS_labelled.svg"
plot_lineage_dist_combined_dm_om_L = paste0(plotdir,"/", lineage_dist_combined_dm_om_L)
#======================================================================== #========================================================================
########################### ###########################
@ -76,7 +80,8 @@ plot_lineage_dist_combined_dm_om = paste0(plotdir,"/", lineage_dist_combined_d
my_df = merged_df2 my_df = merged_df2
# delete variables not required # delete variables not required
rm(my_df_u, merged_df2, merged_df2_comp, merged_df3, merged_df3_comp) rm(my_df_u, merged_df2, merged_df2_comp, merged_df3, merged_df3_comp
, merged_df2_lig, merged_df2_comp_lig, merged_df3_lig, merged_df3_comp_lig)
# quick checks # quick checks
colnames(my_df) colnames(my_df)
@ -153,6 +158,7 @@ table(df_lin$lineage_labels) == table(df_lin$lineage)
#======================== #========================
# mutation_info: labels # mutation_info: labels
#======================== #========================
#{Result:No of DM and OM muts in selected lineages}
table(df_lin$mutation_info) table(df_lin$mutation_info)
df_lin$mutation_info_labels = ifelse(df_lin$mutation_info == dr_muts_col, "DM", "OM") df_lin$mutation_info_labels = ifelse(df_lin$mutation_info == dr_muts_col, "DM", "OM")
@ -163,16 +169,16 @@ table(df_lin$mutation_info) == table(df_lin$mutation_info_labels)
#======================= #=======================
# subset dr muts only # subset dr muts only
#======================= #=======================
my_df_dr = subset(df_lin, mutation_info == dr_muts_col) #my_df_dr = subset(df_lin, mutation_info == dr_muts_col)
table(my_df_dr$mutation_info) #table(my_df_dr$mutation_info)
table(my_df_dr$lineage) #table(my_df_dr$lineage)
#========================= #=========================
# subset other muts only # subset other muts only
#========================= #=========================
my_df_other = subset(df_lin, mutation_info == other_muts_col) #my_df_other = subset(df_lin, mutation_info == other_muts_col)
table(my_df_other$mutation_info) #table(my_df_other$mutation_info)
table(my_df_other$lineage) #table(my_df_other$lineage)
######################################################################## ########################################################################
# end of data extraction and cleaning for plots # # end of data extraction and cleaning for plots #
@ -283,78 +289,29 @@ p2
######################################################################## ########################################################################
#============== #==============
# combine plot # combine plots
#=============== #===============
# 1) without labels
plot_lineage_dist_combined_dm_om plot_lineage_dist_combined_dm_om
svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6) svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6)
printFile = cowplot::plot_grid(p1, p2 OutPlot1 = cowplot::plot_grid(p1, p2
, rel_widths = c(0.5/2, 0.5/2) , rel_widths = c(0.5/2, 0.5/2))
, label_size = my_als+10)
print(printFile) print(OutPlot1)
dev.off() dev.off()
######################################################################## # 2) with labels
# alternate combination plot_lineage_dist_combined_dm_om_L
######################################################################## svg(plot_lineage_dist_combined_dm_om_L, width = 12, height = 6)
#=======================
# Plot 3: lineage dist: geom_density_ridges_gradient (allows aesthetics to vary along ridgeline, no alpha setting!)
# else same as geom_density_ridges)
# x = duet_scaled
# y = duet_outcome
# FACET (f) = lineage
#=======================
# output individual svg OutPlot2 = cowplot::plot_grid(p1, p2
#plot_lineage_dist_duet = paste0(plotdir,"/", "lineage_dist_duet_f.svg") , labels = c("(a)", "(b)")
#plot_lineage_dist_duet
#svg(plot_lineage_dist_duet)
p3 = ggplot(df, aes(x = duet_scaled
, y = duet_outcome))+
geom_density_ridges_gradient(aes(fill = ..x..)
, scale = 3
, size = 0.3) +
facet_wrap( ~lineage_labels
, scales = "free"
#, labeller = labeller(lineage = my_labels) # sorted by lineage_labels
) +
coord_cartesian( xlim = c(-1, 1)) +
scale_fill_gradientn(colours = my_palette, name = "DUET") +
theme(axis.text.x = element_text(size = my_ats
, angle = 90
, hjust = 1
, vjust = 0.4)
, axis.text.y = element_blank()
, axis.title.x = element_text(size = my_ats)
, axis.title.y = element_blank()
, axis.ticks.y = element_blank()
, plot.title = element_blank()
, strip.text = element_text(size = my_als)
, legend.text = element_text(size = my_als-6)
, legend.title = element_text(size = my_als-3))+
labs(x = "DUET")
print(p3)
#dev.off()
#==============
# combine plot: alt version
#===============
plot_lineage_dist_duet_fandnf = paste0(plotdir,"/", "lineage_dist_duet_fandnf.svg")
plot_lineage_dist_duet_fandnf
svg(plot_lineage_dist_duet_fandnf, width = 12, height = 6)
printFile = cowplot::plot_grid(p3, p2
, rel_widths = c(0.5/2, 0.5/2) , rel_widths = c(0.5/2, 0.5/2)
, label_size = my_als+10) , label_size = my_als)
print(printFile) print(OutPlot2)
dev.off() dev.off()
##############################################################################