112 lines
3 KiB
R
Executable file
112 lines
3 KiB
R
Executable file
#!/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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source("~/git/LSHTM_analysis/scripts/Header_TT.R")
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drug = 'streptomycin'
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gene = 'gid'
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spec = matrix(c(
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"drug" , "d", 1, "character",
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"gene" , "g", 1, "character",
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"data_file1" , "fa", 2, "character",
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"data_file2" , "fb", 2, "character"
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), byrow = TRUE, ncol = 4)
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opt = getopt(spec)
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drug = opt$drug
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gene = opt$gene
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infile_params = opt$data_file1
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infile_metadata = opt$data_file2
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if(is.null(drug)|is.null(gene)) {
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stop("Missing arguments: --drug and --gene must both be specified (case-sensitive)")
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}
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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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#===========
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# output
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#===========
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# PS
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bp_subcols_duet = "barplot_coloured_PS.svg"
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plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)
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##############################################################################
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# add frequency of positions (from lib data.table)
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setDT(subcols_df_ps)[, pos_count := .N, by = .(position)]
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foo = data.frame(subcols_df_ps$mutationinformation
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, subcols_df_ps$position
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, subcols_df_ps$pos_count)
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#snpsBYpos_df <- subcols_df_ps %>%
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# group_by(position) %>%
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# summarize(snpsBYpos = mean(pos_count))
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#********************
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# generate plot: PS
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# NO axis colours
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#********************
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g = ggplot(subcols_df_ps
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, aes(x = factor(position, ordered = T)))
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g2 = g + geom_bar()
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g2
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foo = g2 + geom_text(stat='count', aes(label = ..count..))
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foo
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######
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bp_subcols_duet = "TEST_PS.svg"
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plot_bp_subcols_duet = paste0(plotdir, "/", bp_subcols_duet)
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print(paste0("plot name:", plot_bp_subcols_duet))
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svg(plot_bp_subcols_duet, width = 26, height = 4)
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g1 = ggplot(subcols_df_ps, aes(x = factor(position, ordered = T)
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, y = pos_count)) +
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geom_bar(stat = "summary"
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, aes(fill = group), colour = "grey") +
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###################################
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g = ggplot(subcols_df_ps
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, aes(x = factor(position, ordered = T)))
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outPlot_bp_ps = g +
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geom_bar(aes(fill = group), colour = "grey") +
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scale_fill_manual( values = subcols_ps
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, guide = "none") +
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theme( axis.text.x = element_text(size = my_xaxls
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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_yaxls
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.x = element_text(size = my_xaxts)
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, axis.title.y = element_text(size = my_yaxts ) ) +
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labs(title = ""
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#title = my_title
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, x = "Position"
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, y = "Frequency")
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print(outPlot_bp_ps)
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#dev.off()
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######################################################################=
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# End of script
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######################################################################=
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