From a5b03e53e8aa0b6d7517f94ec58c6d40e18853ea Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Wed, 16 Sep 2020 15:37:56 +0100 Subject: [PATCH] updated with two outputs: labelled and unlabelled --- .../plotting/lineage_dist_dm_om_combined_PS.R | 95 +++++-------------- 1 file changed, 26 insertions(+), 69 deletions(-) diff --git a/scripts/plotting/lineage_dist_dm_om_combined_PS.R b/scripts/plotting/lineage_dist_dm_om_combined_PS.R index 37e8cbe..6aa883e 100644 --- a/scripts/plotting/lineage_dist_dm_om_combined_PS.R +++ b/scripts/plotting/lineage_dist_dm_om_combined_PS.R @@ -16,6 +16,7 @@ getwd() source("Header_TT.R") library(ggridges) +library(plyr) source("combining_dfs_plotting.R") # PS combined: # 1) merged_df2 @@ -61,6 +62,9 @@ cat("cols imported:" #======= 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) + +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 # 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 colnames(my_df) @@ -153,6 +158,7 @@ table(df_lin$lineage_labels) == table(df_lin$lineage) #======================== # mutation_info: labels #======================== +#{Result:No of DM and OM muts in selected lineages} table(df_lin$mutation_info) df_lin$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$mutation_info_labels) #======================= # subset dr muts only #======================= -my_df_dr = subset(df_lin, mutation_info == dr_muts_col) -table(my_df_dr$mutation_info) -table(my_df_dr$lineage) +#my_df_dr = subset(df_lin, mutation_info == dr_muts_col) +#table(my_df_dr$mutation_info) +#table(my_df_dr$lineage) #========================= # subset other muts only #========================= -my_df_other = subset(df_lin, mutation_info == other_muts_col) -table(my_df_other$mutation_info) -table(my_df_other$lineage) +#my_df_other = subset(df_lin, mutation_info == other_muts_col) +#table(my_df_other$mutation_info) +#table(my_df_other$lineage) ######################################################################## # 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 svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6) -printFile = cowplot::plot_grid(p1, p2 - , rel_widths = c(0.5/2, 0.5/2) - , label_size = my_als+10) +OutPlot1 = cowplot::plot_grid(p1, p2 + , rel_widths = c(0.5/2, 0.5/2)) -print(printFile) +print(OutPlot1) dev.off() -######################################################################## -# alternate combination -######################################################################## -#======================= -# 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 -#======================= +# 2) with labels +plot_lineage_dist_combined_dm_om_L +svg(plot_lineage_dist_combined_dm_om_L, width = 12, height = 6) -# output individual svg -#plot_lineage_dist_duet = paste0(plotdir,"/", "lineage_dist_duet_f.svg") -#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 +OutPlot2 = cowplot::plot_grid(p1, p2 + , labels = c("(a)", "(b)") , rel_widths = c(0.5/2, 0.5/2) - , label_size = my_als+10) + , label_size = my_als) -print(printFile) +print(OutPlot2) dev.off() - +############################################################################## \ No newline at end of file