Mercurial > repos > artbio > sr_bowtie_dataset_annotation
comparison barplot.r @ 4:e11f91575af6 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie_dataset_annotation commit 618a7892f6af26278364a75ab23b3c6d8cdc73db
author | artbio |
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date | Wed, 20 Mar 2019 07:12:53 -0400 |
parents | 008de522b3ea |
children | 8829656d6999 |
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3:008de522b3ea | 4:e11f91575af6 |
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9 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) | 9 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } ) |
10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") | 10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
11 warnings() | 11 warnings() |
12 library(optparse) | 12 library(optparse) |
13 library(ggplot2) | 13 library(ggplot2) |
14 library(scales) | 14 library(ggrepel) |
15 | |
16 | 15 |
17 | 16 |
18 #Arguments | 17 #Arguments |
19 option_list = list( | 18 option_list = list( |
20 make_option( | 19 make_option( |
35 args = commandArgs(trailingOnly = TRUE)) | 34 args = commandArgs(trailingOnly = TRUE)) |
36 | 35 |
37 | 36 |
38 ## | 37 ## |
39 annotations = read.delim(opt$input, header=F) | 38 annotations = read.delim(opt$input, header=F) |
40 colnames(annotations) = c("class", "counts") | 39 colnames(annotations) = c("sample", "class", "percent_of_reads", "total") |
41 annotations = cbind(annotations, fraction=annotations$counts/annotations$counts[1]) | 40 annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2) |
42 annotations = annotations[-1,] | |
43 # ggplot2 plotting | 41 # ggplot2 plotting |
44 ggplot(annotations, aes(x="classes", y=fraction, fill=class)) + | |
45 geom_bar(width = .7, position=position_stack(), stat = "identity") + | |
46 geom_text(aes(label = percent(fraction)), position = position_stack(vjust = 0.5),size = 4) | |
47 ggtitle('Class proportions') | 42 ggtitle('Class proportions') |
43 ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) + | |
44 geom_bar(position="fill", stat="identity") + | |
45 facet_wrap(~sample, ncol=3 ) + geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) + | |
46 coord_polar(theta="y") + | |
47 labs(x = "Class fractions (%)") + | |
48 theme(axis.text = element_blank(), | |
49 axis.ticks = element_blank(), | |
50 panel.grid = element_blank(), | |
51 axis.title.y = element_blank(), | |
52 legend.position="bottom") + | |
53 geom_text(aes(x = total/2, y= .5, label = paste(round(total/1000000, digits=3), "M"), vjust = 4, hjust=-1), size=2) | |
48 ggsave(file=opt$barplot, device="pdf") | 54 ggsave(file=opt$barplot, device="pdf") |
55 |