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