replaced old lineage barplot with count and diversity combined plots sourced from function
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50b89cdcd7
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7 changed files with 217 additions and 366 deletions
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@ -23,7 +23,7 @@ plot_basic_bp_combined_labelled = paste0(plotdir,"/", basic_bp_combined_labell
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#=======================================================================
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#=======
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# combin DUET and Ligand affinity plots
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# combine DUET and Ligand affinity plots
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#=======
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svg(plot_basic_bp_combined_labelled , width = 12, height = 12 )
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@ -1,214 +0,0 @@
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#!/usr/bin/env Rscript
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting/")
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getwd()
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#########################################################
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# TASK: Basic lineage barplot showing numbers
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# Output: Basic barplot with lineage samples and mut count
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##########################################################
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# Installing and loading required packages
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##########################################################
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source("Header_TT.R")
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require(data.table)
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source("combining_dfs_plotting.R")
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# should return the following dfs, directories and variables
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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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# input
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#===========
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# output of combining_dfs_plotting.R
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#=======
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# output
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#=======
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# plot 1
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basic_bp_lineage = "basic_lineage_barplot.svg"
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plot_basic_bp_lineage = paste0(plotdir,"/", basic_bp_lineage)
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#=======================================================================
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#================
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# Data for plots:
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# you need merged_df2, comprehensive one
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# since this has one-many relationship
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# i.e the same SNP can belong to multiple lineages
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#================
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# REASSIGNMENT as necessary
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my_df = merged_df2
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# clear excess variable
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rm(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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#==========================
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# Plot: Lineage barplot
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# x = lineage y = No. of samples
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# col = Lineage
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# fill = lineage
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#============================
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table(my_df$lineage)
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as.data.frame(table(my_df$lineage))
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#=============
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# Data for plots
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#=============
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# REASSIGNMENT
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df <- my_df
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rm(my_df)
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# get freq count of positions so you can subset freq<1
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#setDT(df)[, lineage_count := .N, by = .(lineage)]
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#******************
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# generate plot: barplot of mutation by lineage
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#******************
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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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df_lin = subset(df, subset = lineage %in% sel_lineages)
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# Create df with lineage inform & no. of unique mutations
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# per lineage and total samples within lineage
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# this is essentially barplot with two y axis
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bar = bar = as.data.frame(sel_lineages) #4, 1
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total_snps_u = NULL
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total_samples = NULL
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for (i in sel_lineages){
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#print(i)
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curr_total = length(unique(df$id)[df$lineage==i])
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total_samples = c(total_samples, curr_total)
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print(total_samples)
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foo = df[df$lineage==i,]
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print(paste0(i, "======="))
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print(length(unique(foo$mutationinformation)))
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curr_count = length(unique(foo$mutationinformation))
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total_snps_u = c(total_snps_u, curr_count)
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}
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print(total_snps_u)
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bar$num_snps_u = total_snps_u
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bar$total_samples = total_samples
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bar
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#*****************
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# generate plot: lineage barplot with two y-axis
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#https://stackoverflow.com/questions/13035295/overlay-bar-graphs-in-ggplot2
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#*****************
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y1 = bar$num_snps_u
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y2 = bar$total_samples
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x = sel_lineages
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to_plot = data.frame(x = x
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, y1 = y1
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, y2 = y2)
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to_plot
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# FIXME later: will be depricated!
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melted = melt(to_plot, id = "x")
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melted
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svg(plot_basic_bp_lineage)
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my_ats = 20 # axis text size
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my_als = 22 # axis label size
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g = ggplot(melted, aes(x = x
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, y = value
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, fill = variable))
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printFile = g + geom_bar(stat = "identity"
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, position = position_stack(reverse = TRUE)
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, alpha=.75
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, colour='grey75') +
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theme(axis.text.x = element_text(size = my_ats)
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, axis.text.y = element_text(size = my_ats
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#, angle = 30
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = my_als
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, colour = 'black')
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, axis.title.y = element_text(size = my_als
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, colour = 'black')
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, legend.position = "top"
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, legend.text = element_text(size = my_als)) +
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#geom_text() +
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geom_label(aes(label = value)
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, size = 5
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, hjust = 0.5
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, vjust = 0.5
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, colour = 'black'
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, show.legend = FALSE
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#, check_overlap = TRUE
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, position = position_stack(reverse = T)) +
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labs(title = ''
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, x = ''
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, y = "Number"
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, fill = 'Variable'
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, colour = 'black') +
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scale_fill_manual(values = c('grey50', 'gray75')
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, name=''
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, labels=c('Mutations', 'Total Samples')) +
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scale_x_discrete(breaks = c('lineage1', 'lineage2', 'lineage3', 'lineage4')
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, labels = c('Lineage 1', 'Lineage 2', 'Lineage 3', 'Lineage 4'))
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print(printFile)
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dev.off()
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128
scripts/plotting/lineage_basic_barplots_combined.R
Normal file
128
scripts/plotting/lineage_basic_barplots_combined.R
Normal file
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@ -0,0 +1,128 @@
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#!/usr/bin/env Rscript
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getwd()
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setwd("~/git/LSHTM_analysis/scripts/plotting/")
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getwd()
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#########################################################
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# TASK: Basic lineage barplot showing numbers
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# Output: Basic barplot with lineage samples and mut count
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##########################################################
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# Installing and loading required packages
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##########################################################
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source("Header_TT.R")
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source("../functions/bp_lineage.R")
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#===========
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# input
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#===========
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source ('get_plotting_dfs.R')
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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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, "\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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# plot 1
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basic_bp_lineage_cl = "basic_lineage_barplots_combined.svg"
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plot_basic_bp_lineage_cl = paste0(plotdir,"/", basic_bp_lineage_cl)
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plot_basic_bp_lineage_cl
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#################################################################
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#=============================
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# PLOT 1: Lineage count plot:
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# LF data
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#=============================
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#------------------------
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# Data: All lineages or
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# selected few
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#------------------------
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sel_lineages = levels(lin_lf$sel_lineages_f)[1:4]
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sel_lineages
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lin_lf_plot = lin_lf[lin_lf$sel_lineages_f%in%sel_lineages,]
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str(lin_lf_plot)
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# drop unused factor levels
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lin_lf_plot$sel_lineages_f = factor(lin_lf_plot$sel_lineages_f)
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levels(lin_lf_plot$sel_lineages_f)
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str(lin_lf_plot)
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#------------------------
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# plot from my function:
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#------------------------
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lin_countP = lin_count_bp(lin_lf_plot
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, x_categ = "sel_lineages_f"
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, y_count = "p_count"
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, bar_fill_categ = "count_categ"
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, display_label_col = "p_count"
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, bar_stat_stype = "identity"
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, x_lab_angle = 90
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, my_xats = 20
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, bar_col_labels = c("Mutations", "Total Samples")
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, bar_col_values = c("grey50", "gray75")
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, y_scale_percent = F # T for diversity
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, y_log10 = F
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, y_label = "Count")
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lin_countP
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#================================
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# PLOT 2: Lineage Diversity plot
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# WF data
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#================================
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#------------------------
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# Data: All lineages or
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# selected few
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#------------------------
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sel_lineages = levels(lin_wf$sel_lineages_f)[1:4]
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sel_lineages
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lin_wf_plot = lin_wf[lin_wf$sel_lineages_f%in%sel_lineages,]
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str(lin_wf_plot)
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# drop unused factor levels
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lin_wf_plot$sel_lineages_f = factor(lin_wf_plot$sel_lineages_f)
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levels(lin_wf_plot$sel_lineages_f)
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str(lin_wf_plot)
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#------------------------
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# plot from my function:
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#------------------------
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lin_diversityP = lin_count_bp(lin_wf_plot
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, x_categ = "sel_lineages_f"
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, y_count = "snp_diversity"
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, display_label_col = "snp_diversity_f"
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, bar_stat_stype = "identity"
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, x_lab_angle = 90
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, my_xats = 20
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, y_scale_percent = T
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, y_label = "SNP diversity")
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lin_diversityP
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#########################################################################333
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#================================
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# Combine plots
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#================================
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svg(plot_basic_bp_lineage_cl , width = 8, height = 15 )
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lineage_bp_combined = cowplot::plot_grid(lin_countP, lin_diversityP
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#, labels = c("(a)", "(b)", "(c)", "(d)")
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, nrow = 2
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, labels = "AUTO"
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, label_size = 25)
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lineage_bp_combined
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dev.off()
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@ -68,42 +68,35 @@ lin_wf
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#=====================
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# SNP diversity
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lin_wf$snp_diversity_f = round( (lin_wf$snp_diversity * 100), digits = 0)
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lin_wf
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lin_wf$snp_diversity_f = paste0(lin_wf$snp_diversity_f, "%")
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# Lineage names
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lin_wf$sel_lineages_f = gsub("lineage", "L", lin_wf$sel_lineages)
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lin_wf
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# # Lineage names
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# lin_wf = lin_wf %>%
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# mutate(ordering_category = case_when(
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# sel_lineages_f == "" ~ 0
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# , sel_lineages_f == "L1" ~ 1
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# , sel_lineages_f == "L2" ~ 2
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# , sel_lineages_f == "L3" ~ 3
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# , sel_lineages_f == "L4" ~ 4
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# , sel_lineages_f == "L5" ~ 5
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# , sel_lineages_f == "L6" ~ 6
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# , sel_lineages_f == "L7" ~ 7
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# , sel_lineages_f == "LBOV" ~ 8
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#
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# , sel_lineages_f == "L1;L2" ~ 9
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# , sel_lineages_f == "L1;L3" ~ 10
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# , sel_lineages_f == "L1;L4" ~ 11
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#
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# , sel_lineages_f == "L2;L3" ~ 12
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# , sel_lineages_f == "L2;L3;L4" ~ 13
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# , sel_lineages_f == "L2;L4" ~ 14
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# , sel_lineages_f == "L2;L6" ~ 15
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# , sel_lineages_f == "L2;LBOV" ~ 16
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#
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# , sel_lineages_f == "L3;L4" ~ 17
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#
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# , sel_lineages_f == "L4;L6" ~ 18
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# , sel_lineages_f == "L4;L7" ~ 19
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#
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# , FALSE ~ -1)
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# )
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# Important: Relevel factors so that x-axis categ appear as you want
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lin_wf$sel_lineages_f = factor(lin_wf$sel_lineages_f, c("L1"
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, "L2"
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, "L3"
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, "L4"
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, "L5"
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, "L6"
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, "L7"
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, "LBOV"
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, "L1;L2"
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, "L1;L3"
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, "L1;L4"
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, "L2;L3"
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, "L2;L3;L4"
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, "L2;L4"
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, "L2;L6"
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, "L2;LBOV"
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, "L3;L4"
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, "L4;L6"
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, "L4;L7"
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, ""))
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levels(lin_wf$sel_lineages_f)
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##################################
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# LF data: lineages with
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@ -134,40 +127,27 @@ if ( nrow(lin_lf) == expected_rows ){
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cat("\nFAIL: numbers mismatch"
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, "\nExpected nrow: ", expected_rows)
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}
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#######################################
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# #=====================
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# # Add some formatting
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# #=====================
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# lin_lf$sel_lineages_f = gsub("lineage", "L", lin_lf$sel_lineages)
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# lin_lf
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# Important: Relevel factors so that x-axis categ appear as you want
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lin_lf$sel_lineages_f = factor(lin_lf$sel_lineages_f, c("L1"
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, "L2"
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, "L3"
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, "L4"
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, "L5"
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, "L6"
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, "L7"
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, "LBOV"
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, "L1;L2"
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, "L1;L3"
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, "L1;L4"
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, "L2;L3"
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, "L2;L3;L4"
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, "L2;L4"
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, "L2;L6"
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, "L2;LBOV"
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, "L3;L4"
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, "L4;L6"
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, "L4;L7"
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, ""))
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# lin_lf = lin_lf %>%
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# mutate(ordering_category = case_when(
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# sel_lineages_f == "" ~ 0
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# , sel_lineages_f == "L1" ~ 1
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# , sel_lineages_f == "L2" ~ 2
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# , sel_lineages_f == "L3" ~ 3
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# , sel_lineages_f == "L4" ~ 4
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# , sel_lineages_f == "L5" ~ 5
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# , sel_lineages_f == "L6" ~ 6
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# , sel_lineages_f == "L7" ~ 7
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# , sel_lineages_f == "LBOV" ~ 8
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#
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# , sel_lineages_f == "L1;L2" ~ 9
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# , sel_lineages_f == "L1;L3" ~ 10
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# , sel_lineages_f == "L1;L4" ~ 11
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#
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# , sel_lineages_f == "L2;L3" ~ 12
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# , sel_lineages_f == "L2;L3;L4" ~ 13
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# , sel_lineages_f == "L2;L4" ~ 14
|
||||
# , sel_lineages_f == "L2;L6" ~ 15
|
||||
# , sel_lineages_f == "L2;LBOV" ~ 16
|
||||
#
|
||||
# , sel_lineages_f == "L3;L4" ~ 17
|
||||
#
|
||||
# , sel_lineages_f == "L4;L6" ~ 18
|
||||
# , sel_lineages_f == "L4;L7" ~ 19
|
||||
#
|
||||
# , FALSE ~ -1)
|
||||
# )
|
||||
levels(lin_lf$sel_lineages_f)
|
||||
|
|
|
|||
|
|
@ -112,6 +112,14 @@ note:
|
|||
- fa flag has default if not supplied
|
||||
- fb flag has default if not supplied
|
||||
|
||||
|
||||
#===================
|
||||
# Add LINEAGE ONE
|
||||
#===================
|
||||
# Lineage_bp.R
|
||||
creates Count and Diversity plot
|
||||
|
||||
|
||||
########################################################################
|
||||
# TODO
|
||||
Delete: dirs.R
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue