/usr/bin/create_pan_genome_plots is in roary 3.8.0+dfsg-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 | #!/usr/bin/env Rscript
# ABSTRACT: Create R plots
# PODNAME: create_plots.R
# Take the output files from the pan genome pipeline and create nice plots.
library(ggplot2)
mydata = read.table("number_of_new_genes.Rtab")
boxplot(mydata, data=mydata, main="Number of new genes",
xlab="No. of genomes", ylab="No. of genes",varwidth=TRUE, ylim=c(0,max(mydata)), outline=FALSE)
mydata = read.table("number_of_conserved_genes.Rtab")
boxplot(mydata, data=mydata, main="Number of conserved genes",
xlab="No. of genomes", ylab="No. of genes",varwidth=TRUE, ylim=c(0,max(mydata)), outline=FALSE)
mydata = read.table("number_of_genes_in_pan_genome.Rtab")
boxplot(mydata, data=mydata, main="No. of genes in the pan-genome",
xlab="No. of genomes", ylab="No. of genes",varwidth=TRUE, ylim=c(0,max(mydata)), outline=FALSE)
mydata = read.table("number_of_unique_genes.Rtab")
boxplot(mydata, data=mydata, main="Number of unique genes",
xlab="No. of genomes", ylab="No. of genes",varwidth=TRUE, ylim=c(0,max(mydata)), outline=FALSE)
mydata = read.table("blast_identity_frequency.Rtab")
plot(mydata,main="Number of blastp hits with different percentage identity", xlab="Blast percentage identity", ylab="No. blast results")
library(ggplot2)
conserved = colMeans(read.table("number_of_conserved_genes.Rtab"))
total = colMeans(read.table("number_of_genes_in_pan_genome.Rtab"))
genes = data.frame( genes_to_genomes = c(conserved,total),
genomes = c(c(1:length(conserved)),c(1:length(conserved))),
Key = c(rep("Conserved genes",length(conserved)), rep("Total genes",length(total))) )
ggplot(data = genes, aes(x = genomes, y = genes_to_genomes, group = Key, linetype=Key)) +geom_line()+
theme_classic() +
ylim(c(1,max(total)))+
xlim(c(1,length(total)))+
xlab("No. of genomes") +
ylab("No. of genes")+ theme_bw(base_size = 16) + theme(legend.justification=c(0,1),legend.position=c(0,1))+
ggsave(filename="conserved_vs_total_genes.png", scale=1)
######################
unique_genes = colMeans(read.table("number_of_unique_genes.Rtab"))
new_genes = colMeans(read.table("number_of_new_genes.Rtab"))
genes = data.frame( genes_to_genomes = c(unique_genes,new_genes),
genomes = c(c(1:length(unique_genes)),c(1:length(unique_genes))),
Key = c(rep("Unique genes",length(unique_genes)), rep("New genes",length(new_genes))) )
ggplot(data = genes, aes(x = genomes, y = genes_to_genomes, group = Key, linetype=Key)) +geom_line()+
theme_classic() +
ylim(c(1,max(unique_genes)))+
xlim(c(1,length(unique_genes)))+
xlab("No. of genomes") +
ylab("No. of genes")+ theme_bw(base_size = 16) + theme(legend.justification=c(1,1),legend.position=c(1,1))+
ggsave(filename="unique_vs_new_genes.png", scale=1)
__END__
=pod
=encoding UTF-8
=head1 NAME
create_plots.R - Create R plots
=head1 VERSION
version 3.8.0
=head1 AUTHOR
Andrew J. Page <ap13@sanger.ac.uk>
=head1 COPYRIGHT AND LICENSE
This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.
This is free software, licensed under:
The GNU General Public License, Version 3, June 2007
=cut
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