106 lines
3.5 KiB
R
Executable file
106 lines
3.5 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("Header_TT.R")
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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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logo_or_plotname = "logo_or_plot.svg"
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plot_logo_or = paste0(plotdir,"/", logo_or_plotname)
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logo_logOR_plotname = "logo_logOR_plot.svg"
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plot_logo_logOR = paste0(plotdir,"/", logo_logOR_plotname)
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##############################################################################
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#================================
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# Logo plot: custom height (OR)
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#================================
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cat("Logo plot with OR as y axis:", plot_logo_or)
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svg(plot_logo_or, width = 30 , height = 6)
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logo_or = ggseqlogo(wide_df_or
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, method = "custom"
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, seq_type = "aa") + ylab("my custom height") +
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theme( axis.text.x = element_text(size = 12
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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 = 22
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.y = element_text(size = 25)
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, axis.title.x = element_text(size = 20)
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#, legend.position = "bottom") +
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, legend.position = "none")+
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#, legend.text = element_text(size = 15)
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#, legend.title = element_text(size = 15))+
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scale_x_discrete("Position"
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#, breaks
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, labels = position_or
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, limits = factor(1:length(position_or))) +
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ylab("Odds Ratio")
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print(logo_or)
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dev.off()
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#=======================================
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# Logo plot: custom height (Log10 OR)
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#=======================================
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cat("Logo plot with log10 OR as y axis:", plot_logo_logOR)
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svg(plot_logo_logOR, width = 30 , height = 6)
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logo_logOR = ggseqlogo(wide_df_logor_m
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, method = "custom"
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, seq_type="aa") + ylab("my custom height") +
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theme(legend.position = "bottom"
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, axis.text.x = element_text(size = 13
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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 = 20
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, angle = 0
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, hjust = 1
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, vjust = 0)
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, axis.title.y = element_text(size = 25)
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, axis.title.x = element_text(size = 20))+
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scale_x_discrete("Position"
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#, breaks
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, labels = position_logor
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, limits = factor(1:length(position_logor)))+
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ylab("Log (Odds Ratio)") +
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scale_y_continuous(limits = c(0, 9))
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print(logo_logOR)
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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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