Mercurial > repos > artbio > sr_bowtie_dataset_annotation
changeset 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 | 279fdd92a615 |
| children | 3bddd7ab96e3 |
| files | barplot.r sr_bowtie_dataset_annotation.xml test-data/multisample5_output.pdf test-data/sample1_output.pdf test-data/sample_output.pdf |
| diffstat | 5 files changed, 15 insertions(+), 2 deletions(-) [+] |
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--- a/barplot.r Sun Mar 24 18:23:00 2019 -0400 +++ b/barplot.r Mon Oct 07 08:40:41 2019 -0400 @@ -12,6 +12,7 @@ library(optparse) library(ggplot2) library(ggrepel) +library(RColorBrewer) #Arguments @@ -39,12 +40,24 @@ colnames(annotations) = c("sample", "class", "percent_of_reads", "total") annotations$percent=round(annotations$percent_of_reads/annotations$total*100, digits=2) # ggplot2 plotting + +# Define the number of colors you want +Sasha.Trubetskoy.Palette <- c('#e6194b', '#3cb44b', '#ffe119', '#4363d8', '#f58231', + '#911eb4', '#46f0f0', '#f032e6', '#bcf60c', + '#008080', '#e6beff', '#9a6324', '#fffac8', '#800000', + '#aaffc3', '#808000', '#ffd8b1', '#000075', '#808080') +nb.cols <- 19 # 10 with colorRampPalette +# mycolors <- colorRampPalette(brewer.pal(8, "Paired"))(nb.cols) +mycolors <- Sasha.Trubetskoy.Palette[1:nb.cols] + ggtitle('Class proportions') ggplot(annotations, aes(x=total/2, y = percent_of_reads, fill = class, width = total)) + geom_bar(position="fill", stat="identity") + - facet_wrap(~sample, ncol=3 ) + geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) + + facet_wrap(~sample, ncol=3 ) + + geom_label_repel(aes(label = percent), position = position_fill(vjust = 0.5), size=2,show.legend = F) + coord_polar(theta="y") + labs(x = "Class fractions (%)") + + scale_fill_manual(values = mycolors) + theme(axis.text = element_blank(), axis.ticks = element_blank(), panel.grid = element_blank(),
--- a/sr_bowtie_dataset_annotation.xml Sun Mar 24 18:23:00 2019 -0400 +++ b/sr_bowtie_dataset_annotation.xml Mon Oct 07 08:40:41 2019 -0400 @@ -1,4 +1,4 @@ -<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.3.0"> +<tool id="sr_bowtie_dataset_annotation" name="Annotate smRNA dataset" version="2.4.0"> <description>by iterative alignments with sRbowtie</description> <requirements> <requirement type="package" version="1.1.2">bowtie</requirement>