Mercurial > repos > artbio > sr_bowtie_dataset_annotation

annotate barplot.r @ 0:bfe92ceffe57 draft

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"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
author artbio
date Mon, 07 Oct 2019 08:40:15 -0400
parents
children 19ba2e38e8ec
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bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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1 if (length(commandArgs(TRUE)) == 0) {
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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2 system("Rscript barplot.r -h", intern = F)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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3 q("no")
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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4 }
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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5
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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7 # load packages that are provided in the conda env
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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8 options( show.error.messages=F,
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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9 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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11 warnings()
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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12 library(optparse)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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13 library(ggplot2)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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14 library(ggrepel)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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15 library(RColorBrewer)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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18 #Arguments
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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19 option_list = list(
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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20 make_option(
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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21 c("-i", "--input"),
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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22 default = NA,
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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23 type = 'character',
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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24 help = "Input file that contains count data (no header)"
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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25 ),
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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26 make_option(
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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27 c("-o", "--barplot"),
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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28 default = NA,
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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29 type = 'character',
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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30 help = "PDF output file"
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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31 )
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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32 )
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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34 opt = parse_args(OptionParser(option_list = option_list),
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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35 args = commandArgs(trailingOnly = TRUE))
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bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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38 ##
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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39 annotations = read.delim(opt$input, header=F)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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40 colnames(annotations) = c("sample", "class", "percent_of_reads", "total")
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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41 annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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42 # ggplot2 plotting
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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44 # Define the number of colors you want
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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45 Sasha.Trubetskoy.Palette <- c('#e6194b', '#3cb44b', '#ffe119', '#4363d8', '#f58231',
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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46 '#911eb4', '#46f0f0', '#f032e6', '#bcf60c',
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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47 '#008080', '#e6beff', '#9a6324', '#fffac8', '#800000',
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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48 '#aaffc3', '#808000', '#ffd8b1', '#000075', '#808080')
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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49 nb.cols <- 19 # 10 with colorRampPalette
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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50 # mycolors <- colorRampPalette(brewer.pal(8, "Paired"))(nb.cols)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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51 mycolors <- Sasha.Trubetskoy.Palette[1:nb.cols]
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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52
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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53 ggtitle('Class proportions')
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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54 ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) +
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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55 geom_bar(position="fill", stat="identity") +
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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56 facet_wrap(~sample, ncol=3 ) +
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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57 geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) +
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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58 coord_polar(theta="y") +
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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59 labs(x = "Class fractions (%)") +
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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60 scale_fill_manual(values = mycolors) +
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61 theme(axis.text = element_blank(),
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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62 axis.ticks = element_blank(),
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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63 panel.grid = element_blank(),
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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64 axis.title.y = element_blank(),
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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65 legend.position="bottom") +
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66 geom_text(aes(x = total/2, y= .5, label = paste(round(total/1000000, digits=3), "M"), vjust = 4, hjust=-1), size=2)
bfe92ceffe57 "planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 60340e9e0d2795b88e23fd57e1ccb190918bf337"
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67 ggsave(file=opt$barplot, device="pdf")
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