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bin/create_pan_genome_plots.R  view on Meta::CPAN

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)

bin/roary-create_pan_genome_plots.R  view on Meta::CPAN

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)

contrib/roary_plots/roary.html  view on Meta::CPAN

<title>roary</title>

<script src="./roary_files/require.min.js"></script>
<script src="./roary_files/jquery.min.js"></script>

<style type="text/css">
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