annotate barplot.r @ 10:fd4a60fc3fca draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit cf30b4fab90cf7910bb2900a05b85ca3344aae59
author artbio
date Tue, 15 Nov 2022 00:45:36 +0000
parents 3bddd7ab96e3
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1 if (length(commandArgs(TRUE)) == 0) {
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fd4a60fc3fca planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit cf30b4fab90cf7910bb2900a05b85ca3344aae59
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2 system("Rscript barplot.r -h", intern = FALSE)
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3 q("no")
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4 }
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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6 # load packages that are provided in the conda env
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fd4a60fc3fca planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit cf30b4fab90cf7910bb2900a05b85ca3344aae59
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7 options(show.error.messages = FALSE,
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8 error = function() {
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9 cat(geterrmessage(), file = stderr())
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fd4a60fc3fca planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit cf30b4fab90cf7910bb2900a05b85ca3344aae59
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10 q("no", 1, FALSE)
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11 }
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12 )
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008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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13 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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14 warnings()
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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15 library(optparse)
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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16 library(ggplot2)
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17 library(ggrepel)
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18 library(RColorBrewer)
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20 option_list <- list(
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21 make_option(
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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22 c("-i", "--input"),
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23 default = NA,
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24 type = "character",
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25 help = "Input file that contains count data (no header)"
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26 ),
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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27 make_option(
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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28 c("-o", "--barplot"),
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29 default = NA,
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30 type = "character",
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31 help = "PDF output file"
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32 )
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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33 )
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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35 opt <- parse_args(OptionParser(option_list = option_list),
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36 args = commandArgs(trailingOnly = TRUE))
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38 annotations <- read.delim(opt$input, header = FALSE)
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39 colnames(annotations) <- c("sample", "class", "percent_of_reads", "total")
3bddd7ab96e3 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 1010eff91c8ce7415d50adaf2f83ecc278295df8"
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40 annotations$percent <- round(annotations$percent_of_reads / annotations$total * 100,
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41 digits = 2)
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42 ## ggplot2 plotting
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44 # Define the number of colors you want
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45 mycolors <- c("#e6194b", "#3cb44b", "#ffe119", "#4363d8", "#f58231",
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46 "#911eb4", "#46f0f0", "#f032e6", "#bcf60c",
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47 "#008080", "#e6beff", "#9a6324", "#fffac8", "#800000",
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48 "#aaffc3", "#808000", "#ffd8b1", "#000075", "#808080")
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49 ggtitle("Class proportions")
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50 ggplot(annotations, aes(x = total / 2, y = percent_of_reads, fill = class, width = total)) +
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51 geom_bar(position = "fill", stat = "identity") +
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52 facet_wrap(~sample, ncol = 3) +
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53 geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5),
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54 size = 2, show.legend = FALSE) +
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55 coord_polar(theta = "y") +
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56 labs(x = "Class fractions (%)") +
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57 scale_fill_manual(values = mycolors) +
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58 theme(axis.text = element_blank(),
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59 axis.ticks = element_blank(),
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60 panel.grid = element_blank(),
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61 axis.title.y = element_blank(),
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62 legend.position = "bottom") +
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63 geom_text(aes(x = total / 2, y = .5, label = paste(round(total / 1000000, digits = 3),
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64 "M"),
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65 vjust = 4, hjust = -1), size = 2)
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66 ggsave(file = opt$barplot, device = "pdf")