Mercurial > repos > artbio > sr_bowtie_dataset_annotation

annotate barplot.r @ 5:279fdd92a615 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 1d30d780dc66069ae9b52c909f65d713156442b3
author artbio
date Sun, 24 Mar 2019 18:23:00 -0400
parents e11f91575af6
children 8829656d6999
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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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1 if (length(commandArgs(TRUE)) == 0) {
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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2 system("Rscript barplot.r -h", intern = F)
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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3 q("no")
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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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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008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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7 # load packages that are provided in the conda env
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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8 options( show.error.messages=F,
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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9 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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10 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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11 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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12 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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13 library(ggplot2)
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e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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14 library(ggrepel)
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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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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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17 #Arguments
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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18 option_list = list(
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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19 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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20 c("-i", "--input"),
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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21 default = NA,
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 type = 'character',
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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23 help = "Input file that contains count data (no header)"
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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24 ),
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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25 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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26 c("-o", "--barplot"),
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 default = NA,
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 type = 'character',
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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29 help = "PDF output file"
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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30 )
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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31 )
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 opt = parse_args(OptionParser(option_list = option_list),
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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34 args = commandArgs(trailingOnly = TRUE))
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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37 ##
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38 annotations = read.delim(opt$input, header=F)
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39 colnames(annotations) = c("sample", "class", "percent_of_reads", "total")
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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40 annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2)
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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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41 # ggplot2 plotting
008de522b3ea planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 53e9bab2c20411f34ac09688de2f2cc8ae8c46a4
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42 ggtitle('Class proportions')
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43 ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) +
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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44 geom_bar(position="fill", stat="identity") +
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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45 facet_wrap(~sample, ncol=3 ) + geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) +
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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46 coord_polar(theta="y") +
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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47 labs(x = "Class fractions (%)") +
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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48 theme(axis.text = element_blank(),
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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49 axis.ticks = element_blank(),
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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50 panel.grid = element_blank(),
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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51 axis.title.y = element_blank(),
e11f91575af6 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
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52 legend.position="bottom") +
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53 geom_text(aes(x = total/2, y= .5, label = paste(round(total/1000000, digits=3), "M"), vjust = 4, hjust=-1), size=2)
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54 ggsave(file=opt$barplot, device="pdf")
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