Mercurial > repos > artbio > sr_bowtie_dataset_annotation
comparison barplot.r @ 6:8829656d6999 draft
"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 08:40:41 -0400 |
| parents | e11f91575af6 |
| children | 3bddd7ab96e3 |
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| 5:279fdd92a615 | 6:8829656d6999 |
|---|---|
| 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(ggrepel) | 14 library(ggrepel) |
| 15 library(RColorBrewer) | |
| 15 | 16 |
| 16 | 17 |
| 17 #Arguments | 18 #Arguments |
| 18 option_list = list( | 19 option_list = list( |
| 19 make_option( | 20 make_option( |
| 37 ## | 38 ## |
| 38 annotations = read.delim(opt$input, header=F) | 39 annotations = read.delim(opt$input, header=F) |
| 39 colnames(annotations) = c("sample", "class", "percent_of_reads", "total") | 40 colnames(annotations) = c("sample", "class", "percent_of_reads", "total") |
| 40 annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2) | 41 annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2) |
| 41 # ggplot2 plotting | 42 # ggplot2 plotting |
| 43 | |
| 44 # Define the number of colors you want | |
| 45 Sasha.Trubetskoy.Palette <- c('#e6194b', '#3cb44b', '#ffe119', '#4363d8', '#f58231', | |
| 46 '#911eb4', '#46f0f0', '#f032e6', '#bcf60c', | |
| 47 '#008080', '#e6beff', '#9a6324', '#fffac8', '#800000', | |
| 48 '#aaffc3', '#808000', '#ffd8b1', '#000075', '#808080') | |
| 49 nb.cols <- 19 # 10 with colorRampPalette | |
| 50 # mycolors <- colorRampPalette(brewer.pal(8, "Paired"))(nb.cols) | |
| 51 mycolors <- Sasha.Trubetskoy.Palette[1:nb.cols] | |
| 52 | |
| 42 ggtitle('Class proportions') | 53 ggtitle('Class proportions') |
| 43 ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) + | 54 ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) + |
| 44 geom_bar(position="fill", stat="identity") + | 55 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) + | 56 facet_wrap(~sample, ncol=3 ) + |
| 57 geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) + | |
| 46 coord_polar(theta="y") + | 58 coord_polar(theta="y") + |
| 47 labs(x = "Class fractions (%)") + | 59 labs(x = "Class fractions (%)") + |
| 60 scale_fill_manual(values = mycolors) + | |
| 48 theme(axis.text = element_blank(), | 61 theme(axis.text = element_blank(), |
| 49 axis.ticks = element_blank(), | 62 axis.ticks = element_blank(), |
| 50 panel.grid = element_blank(), | 63 panel.grid = element_blank(), |
| 51 axis.title.y = element_blank(), | 64 axis.title.y = element_blank(), |
| 52 legend.position="bottom") + | 65 legend.position="bottom") + |