moved old lineage_dist plot scripts to redundant
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2 changed files with 612 additions and 0 deletions
303
scripts/plotting/redundant/lineage_dist_combined_PS.R
Executable file
303
scripts/plotting/redundant/lineage_dist_combined_PS.R
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: Lineage dist plots: ggridges
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# Output: 2 SVGs for PS stability
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# 1) all muts
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# 2) dr_muts
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##########################################################
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# Installing and loading required packages
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##########################################################
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting/")
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getwd()
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source("Header_TT.R")
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library(ggridges)
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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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# 2) merged_df2_comp
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# 3) merged_df3
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# 4) merged_df3_comp
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# LIG combined:
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# 5) merged_df2_lig
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# 6) merged_df2_comp_lig
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# 7) merged_df3_lig
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# 8) merged_df3_comp_lig
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# 9) my_df_u
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# 10) my_df_u_lig
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cat("Directories imported:"
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, "\n===================="
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, "\ndatadir:", datadir
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, "\nindir:", indir
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, "\noutdir:", outdir
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, "\nplotdir:", plotdir)
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cat("Variables imported:"
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, "\n====================="
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, "\ndrug:", drug
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, "\ngene:", gene
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, "\ngene_match:", gene_match
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, "\nAngstrom symbol:", angstroms_symbol
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, "\nNo. of duplicated muts:", dup_muts_nu
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, "\nNA count for ORs:", na_count
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, "\nNA count in df2:", na_count_df2
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, "\nNA count in df3:", na_count_df3
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, "\ndr_muts_col:", dr_muts_col
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, "\nother_muts_col:", other_muts_col
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, "\ndrtype_col:", resistance_col)
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#=======
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# output
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#=======
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lineage_dist_combined = "lineage_dist_combined_PS.svg"
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plot_lineage_dist_combined = paste0(plotdir,"/", lineage_dist_combined)
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#========================================================================
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###########################
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# Data for plots
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# you need merged_df2 or merged_df2_comp
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# since this is one-many relationship
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# i.e the same SNP can belong to multiple lineages
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# using the _comp dataset means
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# we lose some muts and at this level, we should use
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# as much info as available, hence use df with NA
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###########################
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# REASSIGNMENT
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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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# quick checks
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colnames(my_df)
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str(my_df)
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# Ensure correct data type in columns to plot: need to be factor
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is.factor(my_df$lineage)
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my_df$lineage = as.factor(my_df$lineage)
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is.factor(my_df$lineage)
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table(my_df$mutation_info)
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# subset df with dr muts only
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my_df_dr = subset(my_df, mutation_info == "dr_mutations_pyrazinamide")
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table(my_df_dr$mutation_info)
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########################################################################
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# end of data extraction and cleaning for plots #
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########################################################################
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#==========================
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# Plot 1: ALL Muts
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# x = mcsm_values, y = dist
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# fill = stability
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#============================
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my_plot_name = 'lineage_dist_PS.svg'
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plot_lineage_duet = paste0(plotdir,"/", my_plot_name)
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#===================
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# Data for plots
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#===================
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table(my_df$lineage); str(my_df$lineage)
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# subset only lineages1-4
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sel_lineages = c("lineage1"
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, "lineage2"
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, "lineage3"
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, "lineage4"
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#, "lineage5"
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#, "lineage6"
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#, "lineage7"
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)
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# uncomment as necessary
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df_lin = subset(my_df, subset = lineage %in% sel_lineages )
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table(df_lin$lineage)
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# refactor
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df_lin$lineage = factor(df_lin$lineage)
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sum(table(df_lin$lineage)) #{RESULT: Total number of samples for lineage}
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table(df_lin$lineage)#{RESULT: No of samples within lineage}
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length(unique(df_lin$mutationinformation))#{Result: No. of unique mutations the 4 lineages contribute to}
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length(df_lin$mutationinformation)
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u2 = unique(my_df$mutationinformation)
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u = unique(df_lin$mutationinformation)
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check = u2[!u2%in%u]; print(check) #{Muts not present within selected lineages}
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#%%%%%%%%%%%%%%%%%%%%%%%%%
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# REASSIGNMENT
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df <- df_lin
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#%%%%%%%%%%%%%%%%%%%%%%%%%
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rm(df_lin)
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#******************
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# generate distribution plot of lineages
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#******************
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# 2 : ggridges (good!)
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my_ats = 15 # axis text size
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my_als = 20 # axis label size
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my_labels = c('Lineage 1', 'Lineage 2', 'Lineage 3', 'Lineage 4'
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#, 'Lineage 5', 'Lineage 6', 'Lineage 7'
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)
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names(my_labels) = c('lineage1', 'lineage2', 'lineage3', 'lineage4'
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# , 'lineage5', 'lineage6', 'lineage7'
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)
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# check plot name
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plot_lineage_duet
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# output svg
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#svg(plot_lineage_duet)
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p1 = ggplot(df, aes(x = duet_scaled
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, y = duet_outcome))+
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#printFile=geom_density_ridges_gradient(
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geom_density_ridges_gradient(aes(fill = ..x..)
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#, jittered_points = TRUE
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, scale = 3
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, size = 0.3 ) +
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facet_wrap( ~lineage
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, scales = "free"
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#, switch = 'x'
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, labeller = labeller(lineage = my_labels) ) +
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coord_cartesian( xlim = c(-1, 1)) +
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scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4")
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, 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_blank()
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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-5)
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, legend.title = element_text(size = my_als)
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)
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print(p1)
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#dev.off()
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#######################################################################
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# lineage distribution plot for dr_muts
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#######################################################################
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#==========================
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# Plot 2: dr muts ONLY
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# x = mcsm_values, y = dist
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# fill = stability
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#============================
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my_plot_name_dr = 'lineage_dist_dr_muts_PS.svg'
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plot_lineage_dr_duet = paste0(plotdir,"/", my_plot_name_dr)
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#===================
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# Data for plots
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#===================
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table(my_df_dr$lineage); str(my_df_dr$lineage)
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# uncomment as necessary
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df_lin_dr = subset(my_df_dr, subset = lineage %in% sel_lineages)
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table(df_lin_dr$lineage)
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# refactor
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df_lin_dr$lineage = factor(df_lin_dr$lineage)
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sum(table(df_lin_dr$lineage)) #{RESULT: Total number of samples for lineage}
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table(df_lin_dr$lineage)#{RESULT: No of samples within lineage}
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length(unique(df_lin_dr$mutationinformation))#{Result: No. of unique mutations the 4 lineages contribute to}
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length(df_lin_dr$mutationinformation)
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u2 = unique(my_df_dr$mutationinformation)
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u = unique(df_lin_dr$mutationinformation)
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check = u2[!u2%in%u]; print(check) #{Muts not present within selected lineages}
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#%%%%%%%%%%%%%%%%%%%%%%%%%
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# REASSIGNMENT
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df_dr <- df_lin_dr
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#%%%%%%%%%%%%%%%%%%%%%%%%%
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rm(df_lin_dr)
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#******************
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# generate distribution plot of lineages
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#******************
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# 2 : ggridges (good!)
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my_ats = 15 # axis text size
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my_als = 20 # axis label size
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# check plot name
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plot_lineage_dr_duet
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# output svg
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#svg(plot_lineage_dr_duet)
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p2 = ggplot(df_dr, 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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#, jittered_points = TRUE
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, scale = 3
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, size = 0.3) +
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#geom_point(aes(size = or_mychisq))+
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facet_wrap( ~lineage
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, scales = "free"
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#, switch = 'x'
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, labeller = labeller(lineage = my_labels) ) +
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coord_cartesian( xlim = c(-1, 1)
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#, ylim = c(0, 6)
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#, clip = "off"
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) +
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scale_fill_gradientn(colours = c("#f8766d", "white", "#00bfc4")
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, 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_blank()
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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 = 10)
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, legend.title = element_text(size = my_als)
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#, legend.position = "none"
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)
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print(p2)
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#dev.off()
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########################################################################
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#==============
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# combine plot
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#===============
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svg(plot_lineage_dist_combined, width = 12, height = 6)
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printFile = cowplot::plot_grid(p1, p2
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, label_size = my_als+10)
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print(printFile)
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dev.off()
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309
scripts/plotting/redundant/lineage_dist_dm_om_combined_PS.R
Executable file
309
scripts/plotting/redundant/lineage_dist_dm_om_combined_PS.R
Executable file
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@ -0,0 +1,309 @@
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: Lineage dist plots: ggridges
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# Output: 2 SVGs for PS stability
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# 1) all muts
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# 2) dr_muts
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##########################################################
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# Installing and loading required packages
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##########################################################
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting/")
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getwd()
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source("Header_TT.R")
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source("get_plotting_dfs.R")
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cat("cols imported:"
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, mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2)
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#=======
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# output
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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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# Data for plots
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# you need merged_df2 or merged_df2_comp
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# since this is one-many relationship
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# i.e the same SNP can belong to multiple lineages
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# using the _comp dataset means
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# we lose some muts and at this level, we should use
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# as much info as available, hence use df with NA
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###########################
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#===================
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# Data for plots
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#===================
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lin_dist_plot = merged_df2[merged_df2$lineage%in%c("lineage1", "lineage2", "lineage3", "lineage4"),]
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table(lin_dist_plot$lineage)
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#{RESULT: Total number of samples for lineage}
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sum(table(lin_dist_plot$lineage))
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#{RESULT: No of samples within lineage}
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table(lin_dist_plot$lineage)
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#{Result: No. of unique mutations the 4 lineages contribute to}
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length(unique(lin_dist_plot$mutationinformation))
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u2 = unique(lin_dist_plot$mutationinformation)
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u = unique(lin_dist_plot$mutationinformation)
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#{Result:Muts not present within selected lineages}
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check = u2[!u2%in%u]; print(check)
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# workaround to make labels appear nicely for in otherwise cases
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#==================
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# lineage: labels
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# from "plyr"
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#==================
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#{Result:No of samples in selected lineages}
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table(lin_dist_plot$lineage)
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lin_dist_plot$lineage_labels = mapvalues(lin_dist_plot$lineage
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, from = c("lineage1","lineage2", "lineage3", "lineage4")
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, to = c("Lineage 1", "Lineage 2", "Lineage 3", "Lineage 4"))
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table(lin_dist_plot$lineage_labels)
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table(lin_dist_plot$lineage_labels) == table(lin_dist_plot$lineage)
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#========================
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# mutation_info: labels
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#========================
|
||||||
|
#{Result:No of DM and OM muts in selected lineages}
|
||||||
|
table(lin_dist_plot$mutation_info)
|
||||||
|
|
||||||
|
lin_dist_plot$mutation_info_labels = ifelse(lin_dist_plot$mutation_info == dr_muts_col
|
||||||
|
, "DM", "OM")
|
||||||
|
table(lin_dist_plot$mutation_info_labels)
|
||||||
|
|
||||||
|
table(lin_dist_plot$mutation_info) == table(lin_dist_plot$mutation_info_labels)
|
||||||
|
|
||||||
|
#========================
|
||||||
|
# duet_outcome: labels
|
||||||
|
#========================
|
||||||
|
#{Result: No. of D and S mutations in selected lineages}
|
||||||
|
table(lin_dist_plot$duet_outcome)
|
||||||
|
|
||||||
|
lin_dist_plot$duet_outcome_labels = ifelse(lin_dist_plot$duet_outcome == "Destabilising"
|
||||||
|
, "D", "S")
|
||||||
|
table(lin_dist_plot$duet_outcome_labels)
|
||||||
|
|
||||||
|
table(lin_dist_plot$duet_outcome) == table(lin_dist_plot$duet_outcome_labels)
|
||||||
|
|
||||||
|
|
||||||
|
#=======================
|
||||||
|
# subset dr muts only
|
||||||
|
#=======================
|
||||||
|
#my_df_dr = subset(df_lin, mutation_info == dr_muts_col)
|
||||||
|
#table(my_df_dr$mutation_info)
|
||||||
|
#table(my_df_dr$lineage)
|
||||||
|
|
||||||
|
#=========================
|
||||||
|
# subset other muts only
|
||||||
|
#=========================
|
||||||
|
#my_df_other = subset(df_lin, mutation_info == other_muts_col)
|
||||||
|
#table(my_df_other$mutation_info)
|
||||||
|
#table(my_df_other$lineage)
|
||||||
|
|
||||||
|
########################################################################
|
||||||
|
# end of data extraction and cleaning for plots #
|
||||||
|
########################################################################
|
||||||
|
#******************
|
||||||
|
# generate distribution plot of lineages
|
||||||
|
#******************
|
||||||
|
# 2 : ggridges (good!)
|
||||||
|
my_ats = 15 # axis text size
|
||||||
|
my_als = 20 # axis label size
|
||||||
|
n_colours = length(unique(lin_dist_plot$duet_scaled))
|
||||||
|
|
||||||
|
my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2))(n = n_colours+1)
|
||||||
|
|
||||||
|
#=======================================
|
||||||
|
# Plot 1: 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
|
||||||
|
# fill = duet_scaled
|
||||||
|
# Facet: Lineage
|
||||||
|
#=======================================
|
||||||
|
# output individual svg
|
||||||
|
#plot_lineage_dist_duet_f paste0(plotdir,"/", "lineage_dist_duet_f.svg")
|
||||||
|
#plot_lineage_dist_duet_f
|
||||||
|
#svg(plot_lineage_dist_duet_f)
|
||||||
|
|
||||||
|
p1 = ggplot(lin_dist_plot, aes(x = duet_scaled
|
||||||
|
#, y = duet_outcome
|
||||||
|
, y = mutation_info_labels
|
||||||
|
))+
|
||||||
|
geom_density_ridges_gradient(aes(fill = ..x..)
|
||||||
|
#, jittered_points = TRUE
|
||||||
|
, scale = 3
|
||||||
|
, size = 0.3 ) +
|
||||||
|
facet_wrap( ~lineage_labels
|
||||||
|
#~mutation_info_labels
|
||||||
|
# ~mutation_info_labels
|
||||||
|
# , scales = "free"
|
||||||
|
# , labeller = labeller(lineage = my_labels)
|
||||||
|
) +
|
||||||
|
#coord_cartesian( xlim = c(-1, 1)) +
|
||||||
|
scale_x_continuous(expand = c(0.01, 0)) +
|
||||||
|
|
||||||
|
scale_fill_gradientn(colours = my_palette
|
||||||
|
, name = "DUET"
|
||||||
|
#, breaks = c(-1, 0, 1)
|
||||||
|
#, labels = c(-1,0,1)
|
||||||
|
#, limits = c(-1,1)
|
||||||
|
) +
|
||||||
|
theme(axis.text.x = element_text(size = my_ats
|
||||||
|
, angle = 90
|
||||||
|
, hjust = 1
|
||||||
|
, vjust = 0.4)
|
||||||
|
#, axis.text.y = element_blank()
|
||||||
|
, axis.text.y = element_text(size = my_ats)
|
||||||
|
, 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-10)
|
||||||
|
#, legend.title = element_text(size = my_als-6)
|
||||||
|
, legend.title = element_blank()
|
||||||
|
, legend.position = c(-0.08, 0.41)
|
||||||
|
, legend.direction = "horizontal"
|
||||||
|
, legend.position = "top"
|
||||||
|
)+
|
||||||
|
labs(x = "DUET")
|
||||||
|
|
||||||
|
p1
|
||||||
|
|
||||||
|
|
||||||
|
#p1_with_legend = p1 + guides(fill = guide_colourbar(label = FALSE))
|
||||||
|
|
||||||
|
#=======================================
|
||||||
|
# Plot 2: lineage dist: geom_density_ridges, allows alpha to be set
|
||||||
|
# x = duet_scaled
|
||||||
|
# y = lineage_labels
|
||||||
|
# fill = mutation_info
|
||||||
|
# NO FACET
|
||||||
|
#=======================================
|
||||||
|
# output svg
|
||||||
|
#plot_lineage_dist_duet_dm_om = paste0(plotdir,"/", "lineage_dist_duet_dm_om.svg")
|
||||||
|
#plot_lineage_dist_duet_dm_om
|
||||||
|
#svg(plot_lineage_dist_duet_dm_om)
|
||||||
|
|
||||||
|
p2 = ggplot(lin_dist_plot, aes(x = duet_scaled
|
||||||
|
, y = lineage_labels))+
|
||||||
|
geom_density_ridges(aes(fill = factor(mutation_info_labels))
|
||||||
|
, scale = 3
|
||||||
|
, size = 0.3
|
||||||
|
, alpha = 0.8) +
|
||||||
|
scale_x_continuous(expand = c(0.01, 0)) +
|
||||||
|
#coord_cartesian( xlim = c(-1, 1)) +
|
||||||
|
scale_fill_manual(values = c("#E69F00", "#999999")) +
|
||||||
|
theme(axis.text.x = element_text(size = my_ats
|
||||||
|
, angle = 90
|
||||||
|
, hjust = 1
|
||||||
|
, vjust = 0.4)
|
||||||
|
, axis.text.y = element_text(size = my_ats)
|
||||||
|
, 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-4)
|
||||||
|
, legend.title = element_text(size = my_als-4)
|
||||||
|
, legend.position = c(0.8, 0.9)) +
|
||||||
|
labs(x = "DUET"
|
||||||
|
, fill = "Mutation class") # legend title
|
||||||
|
|
||||||
|
p2
|
||||||
|
|
||||||
|
#=======================================
|
||||||
|
# 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 = lineage_labels
|
||||||
|
# fill = duet_scaled
|
||||||
|
# NO FACET (nf)
|
||||||
|
#=======================================
|
||||||
|
# output individual svg
|
||||||
|
#plot_lineage_dist_duet_nf = paste0(plotdir,"/", "lineage_dist_duet_nf.svg")
|
||||||
|
#plot_lineage_dist_duet_nf
|
||||||
|
#svg(plot_lineage_dist_duet_nf)
|
||||||
|
|
||||||
|
p3 = ggplot(lin_dist_plot, aes(x = duet_scaled
|
||||||
|
, y = lineage_labels))+
|
||||||
|
# geom_density_ridges_gradient(aes(fill = ..x..)
|
||||||
|
# #, jittered_points = TRUE
|
||||||
|
# , scale = 3
|
||||||
|
# , size = 0.3 ) +
|
||||||
|
geom_density_ridges()+
|
||||||
|
#facet_wrap (~mutation_info_labels) +
|
||||||
|
#coord_cartesian( xlim = c(-1, 1)) +
|
||||||
|
scale_x_continuous(expand = c(0.01, 0)) +
|
||||||
|
|
||||||
|
#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_text(size = my_ats)
|
||||||
|
, 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-10)
|
||||||
|
, legend.title = element_text(size = my_als-3)
|
||||||
|
, legend.position = c(0.8, 0.8)) +
|
||||||
|
#, legend.direction = "horizontal")+
|
||||||
|
#, legend.position = "top")+
|
||||||
|
labs(x = "DUET")
|
||||||
|
|
||||||
|
p3
|
||||||
|
|
||||||
|
########################################################################
|
||||||
|
#==============
|
||||||
|
# combine plots
|
||||||
|
#===============
|
||||||
|
# 1) without labels
|
||||||
|
plot_lineage_dist_combined_dm_om
|
||||||
|
svg(plot_lineage_dist_combined_dm_om, width = 12, height = 6)
|
||||||
|
|
||||||
|
OutPlot1 = cowplot::plot_grid(p1, p2
|
||||||
|
, rel_widths = c(0.5/2, 0.5/2))
|
||||||
|
|
||||||
|
print(OutPlot1)
|
||||||
|
dev.off()
|
||||||
|
|
||||||
|
|
||||||
|
# 2) with labels
|
||||||
|
plot_lineage_dist_combined_dm_om_L
|
||||||
|
svg(plot_lineage_dist_combined_dm_om_L, width = 12, height = 6)
|
||||||
|
|
||||||
|
OutPlot2 = cowplot::plot_grid(p1, p2
|
||||||
|
#, labels = c("(a)", "(b)")
|
||||||
|
, labels = "AUTO"
|
||||||
|
#, label_x = -0.045, label_y = 0.92
|
||||||
|
#, hjust = -0.7, vjust = -0.5
|
||||||
|
#, align = "h"
|
||||||
|
, rel_widths = c(0.5/2, 0.5/2)
|
||||||
|
, label_size = my_als)
|
||||||
|
|
||||||
|
print(OutPlot2)
|
||||||
|
dev.off()
|
||||||
|
|
||||||
|
##############################################################################
|
||||||
Loading…
Add table
Add a link
Reference in a new issue