added lineage_dist.R nad renamed lineage_bp_data file to lineage_data
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cdab8f0414
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69
scripts/functions/lineage_dist.R
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69
scripts/functions/lineage_dist.R
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###############################
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# TASK: function to plot lineage
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# dist plots with or without facet
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# think about color palette
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# for stability
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##############################
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#n_colours = length(unique(lin_dist_plot$duet_scaled))
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#my_palette <- colorRampPalette(c(mcsm_red2, mcsm_red1, mcsm_mid, mcsm_blue1, mcsm_blue2))(n = n_colours+1)
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lineage_distP <- function(plotdf
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, x_axis = "duet_scaled"
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, y_axis = "lineage_labels"
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, x_lab = "DUET"
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, with_facet = F
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, facet_wrap_var = ""
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, fill_categ = "mutation_info_labels"
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, fill_categ_cols = c("#E69F00", "#999999")
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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_leg_ts = 16
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, my_leg_title = 16
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, my_strip_ts = 20
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, leg_pos = c(0.8, 0.9)
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, leg_pos_wf = c("top", "left", "bottom", "right")
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, leg_dir_wf = c("horizontal", "vertical")
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, leg_label = "")
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{
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LinDistP = ggplot(plotdf, aes_string(x = x_axis
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, y = y_axis))+
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geom_density_ridges(aes_string(fill = fill_categ)
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, scale = 3
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, size = 0.3
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, alpha = 0.8) +
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scale_x_continuous(expand = c(0.01, 0.01)) +
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#coord_cartesian( xlim = c(-1, 1)) +
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scale_fill_manual(values = fill_categ_cols) +
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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_text(size = my_ats)
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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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, strip.text = element_text(size = my_strip_ts)
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, legend.text = element_text(size = my_leg_ts)
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, legend.title = element_text(size = my_leg_title)
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, legend.position = c(0.8, 0.9)) +
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labs(x = x_lab
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, fill = leg_label)
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if (with_facet){
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# used reformulate or make as formula
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#fwv = reformulate(facet_wrap_var)
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fwv = as.formula(paste0("~", facet_wrap_var))
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LinDistP = LinDistP +
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facet_wrap(fwv) +
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theme(legend.position = leg_pos_wf
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, legend.direction = leg_dir_wf)
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}
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return(LinDistP)
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}
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155
scripts/plotting/lineage_data.R
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155
scripts/plotting/lineage_data.R
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#!/usr/bin/env Rscript
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#########################################################
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# TASK: Script to format data for lineage barplots:
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# WF and LF data with lineage sample, and snp counts
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# sourced by get_plotting_dfs.R
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#########################################################
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# working dir and loading libraries
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# getwd()
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# setwd("~/git/LSHTM_analysis/scripts/plotting")
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# getwd()
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# make cmd
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# globals
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# drug = "streptomycin"
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# gene = "gid"
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# source("get_plotting_dfs.R")
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#=======================================================================
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#################################################
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# Get data with lineage count, and snp diversity
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#################################################
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table(merged_df2$lineage)
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if (table(merged_df2$lineage == "")[[2]]) {
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cat("\nMissing samples with lineage classification:", table(merged_df2$lineage == "")[[2]])
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}
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table(merged_df2$lineage_labels)
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class(merged_df2$lineage_labels); nlevels(merged_df2$lineage_labels)
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##################################
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# WF data: lineages with
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# snp count
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# total_samples
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# snp diversity (perc)
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##################################
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sel_lineages = levels(merged_df2$lineage_labels)
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lin_wf = 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(merged_df2$id)[merged_df2$lineage_labels==i])
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#print(curr_total)
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total_samples = c(total_samples, curr_total)
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print(total_samples)
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foo = merged_df2[merged_df2$lineage_labels==i,]
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print(paste0(i, "=======\n"))
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print(length(unique(foo$mutationinformation)))
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curr_count = length(unique(foo$mutationinformation))
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total_snps_u = c(total_snps_u, curr_count)
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}
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lin_wf
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# Add these counts as columns to the df
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lin_wf$num_snps_u = total_snps_u
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lin_wf$total_samples = total_samples
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lin_wf
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# Add SNP diversity
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lin_wf$snp_diversity = lin_wf$num_snps_u/lin_wf$total_samples
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lin_wf
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#=====================
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# Add some formatting
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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$snp_diversity_f = paste0(lin_wf$snp_diversity_f, "%")
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lin_wf$sel_lineages
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# Important: Check factors so that x-axis categ appear as you want
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lin_wf$sel_lineages = factor(lin_wf$sel_lineages, c("L1"
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, "L2"
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, "L3"
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, "L4"
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, "L5"
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, "L6"
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, "L7"
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, "LBOV"
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, "L1;L2"
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, "L1;L3"
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, "L1;L4"
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, "L2;L3"
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, "L2;L3;L4"
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, "L2;L4"
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, "L2;L6"
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, "L2;LBOV"
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, "L3;L4"
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, "L4;L6"
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, "L4;L7"
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, ""))
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levels(lin_wf$sel_lineages)
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##################################
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# LF data: lineages with
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# snp count
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# total_samples
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# snp diversity (perc)
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##################################
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names(lin_wf)
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tot_cols = ncol(lin_wf)
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pivot_cols = c("sel_lineages", "snp_diversity", "snp_diversity_f")
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pivot_cols_n = length(pivot_cols)
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expected_rows = nrow(lin_wf) * ( length(lin_wf) - pivot_cols_n )
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lin_lf <- gather(lin_wf
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, count_categ
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, p_count
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, num_snps_u:total_samples
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, factor_key = TRUE)
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lin_lf
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# quick checks
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if ( nrow(lin_lf ) == expected_rows ){
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cat("\nPASS: Lineage LF data created"
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, "\nnrow: ", nrow(lin_lf)
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, "\nncol: ", ncol(lin_lf))
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} else {
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cat("\nFAIL: numbers mismatch"
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, "\nExpected nrow: ", expected_rows)
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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_lf$sel_lineages = factor(lin_lf$sel_lineages, 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_lf$sel_lineages)
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