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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
author artbio
date Sun, 09 May 2021 17:07:22 +0000
parents c3df361bd216
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c3df361bd216 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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1 ## Setup R error handling to go to stderr
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2 options(show.error.messages = F,
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3 error = function() {
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4 cat(geterrmessage(), file = stderr()); q("no", 1, F)
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5 }
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6 )
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7 options(warn = -1)
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9 library(RColorBrewer)
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10 library(lattice)
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11 library(latticeExtra)
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12 library(grid)
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13 library(gridExtra)
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14 library(optparse)
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16 option_list <- list(
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17 make_option(c("-f", "--first_dataframe"), type = "character", help = "path to first dataframe"),
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18 make_option("--first_plot_method", type = "character", help = "How additional data should be plotted"),
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19 make_option("--output_pdf", type = "character", help = "path to the pdf file with plots")
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20 )
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22 parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
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23 args <- parse_args(parser)
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25 # data frames implementation
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27 ## first table
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28 table <- read.delim(args$first_dataframe, header = T, row.names = NULL)
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29 colnames(table)[1] <- "Dataset"
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30 dropcol <- c("Strandness", "z.score") # not used by this Rscript and is dropped for backward compatibility
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31 table <- table[, !(names(table) %in% dropcol)]
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32 if (args$first_plot_method == "Counts" | args$first_plot_method == "Size") {
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33 table <- within(table, Counts[Polarity == "R"] <- (Counts[Polarity == "R"] * -1))
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34 }
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35 n_samples <- length(unique(table$Dataset))
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36 samples <- unique(table$Dataset)
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37 genes <- unique(table$Chromosome)
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38 per_gene_readmap <- lapply(genes, function(x) subset(table, Chromosome == x))
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39 per_gene_limit <- lapply(genes, function(x) c(1, unique(subset(table, Chromosome == x)$Chrom_length)))
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40 n_genes <- length(per_gene_readmap)
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42 ## functions
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43 plot_unit <- function(df, method = args$first_plot_method, ...) {
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44 p <- xyplot(Counts ~ Coordinate | factor(Dataset, levels = unique(Dataset)) + factor(Chromosome, levels = unique(Chromosome)),
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45 data = df,
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46 type = "h",
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47 lwd = 1.5,
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48 scales = list(relation = "free", x = list(rot = 0, cex = 0.7, axs = "i", tck = 0.5), y = list(tick.number = 4, rot = 90, cex = 0.7)),
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49 xlab = NULL, main = NULL, ylab = NULL,
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50 as.table = T,
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51 origin = 0,
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52 horizontal = FALSE,
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53 group = Polarity,
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54 col = c("red", "blue"),
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55 par.strip.text = list(cex = 0.7),
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56 ...)
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57 p <- combineLimits(p)
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58 }
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60 ## function parameters
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61 par_settings_firstplot <- list(layout.heights = list(top.padding = -2, bottom.padding = -2), strip.background = list(col = c("lightblue", "lightgreen")))
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62 title_first_method <- list(Counts = "Read Counts", Coverage = "Coverage depths", Median = "Median sizes", Mean = "Mean sizes", Size = "Size Distributions")
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63 legend_first_method <- list(Counts = "Read count", Coverage = "Coverage depth", Median = "Median size", Mean = "Mean size", Size = "Read count")
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64 bottom_first_method <- list(Counts = "Coordinates (nucleotides)", Coverage = "Coordinates (nucleotides)", Median = "Coordinates (nucleotides)", Mean = "Coordinates (nucleotides)", Size = "Sizes of reads")
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66 ## Plotting Functions
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67 single_plot <- function(...) {
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68 width <- 8.2677 * n_samples / 2
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69 rows_per_page <- 8
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70 graph_heights <- c(rep(40, 8), 10)
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71 pdf(file = args$output_pdf, paper = "special", height = 15, width = width)
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72 for (i in seq(1, n_genes, rows_per_page)) {
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73 start <- i
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74 end <- i + rows_per_page - 1
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75 if (end > n_genes) {
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76 end <- n_genes
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77 }
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78 if (end - start + 1 < 8) {
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79 graph_heights <- c(rep(c(40), end - start + 1), 10, rep(c(40), 8 - (end - start + 1)))
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80 }
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81 first_plot_list <- lapply(per_gene_readmap[start:end], function(x) update(useOuterStrips(plot_unit(x, par.settings = par_settings_firstplot), strip.left = strip.custom(par.strip.text = list(cex = 0.5)))))
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82 plot.list <- rbind(first_plot_list)
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83 args_list <- c(plot.list, list(nrow = rows_per_page + 1, ncol = 1, heights = unit(graph_heights, rep("mm", 9)),
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84 top = textGrob("Cluster Read Counts (Peaks in middle of clusters)", gp = gpar(cex = 1), vjust = 0, just = "top"),
520dd9ee0575 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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85 left = textGrob("Read Counts", gp = gpar(cex = 1), vjust = 0, hjust = 0, x = 1, y = (-0.41 / 7) * (end - start - (6.23 / 0.41)), rot = 90),
520dd9ee0575 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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86 sub = textGrob("Coordinates (nucleotides)", gp = gpar(cex = 1), just = "bottom", vjust = 2)
0
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87 )
c3df361bd216 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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88 )
c3df361bd216 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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89 do.call(grid.arrange, args_list)
c3df361bd216 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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90 }
1
520dd9ee0575 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit 51dc6c56c7d95fc229ffee958354211cd454fd36"
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91 devname <- dev.off()
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92 }
c3df361bd216 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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93
c3df361bd216 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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94 # main
c3df361bd216 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_clusters commit f38805cf151cbda1cf7de0a92cdfeb5978f26547"
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95 single_plot()