Dataset summary and supplemental figures for article: "No evidence known viruses play a role in the pathogenesis of onchocerciasis-associated epilepsy. An explorative metagenomic case control study"

Dataset summary output of Hecatomb pipeline. These files are all you need to reproduce the figures in the manuscript.

# in R

# read data and metadata
data=read.table('big_table.tsv',sep='\t',header=T)
meta=read.table('metadata.tsv',sep='\t',header=T)

# combine
data=merge(data, meta, by.x='sample',by.y='sample_id')

# patients #7 and #14 were excluded
data = data[! data$individual %in% c(7,14),]

# filter (ignore non virus, ignore poor evalue, ignore nt-only hits)
data = data[data$Kingdom=='Viruses' & data$ali_evalue<1e-20 & data$nt_aa=='aa',]

# Figure 1
library(ggplot2)

ggplot(data) + 
    geom_point(aes(x=ali_len, y=ali_perc, color=source, size=count),alpha=0.1) + 
    facet_wrap(~Family) + 
    scale_color_brewer(palette = "Dark2") + 
    theme_bw() + 
    theme(panel.spacing = unit(0,'mm'), 
        strip.background = element_rect(color = 'black',fill = 'white')) + 
    scale_x_continuous(name='Alignment length') + 
    scale_y_continuous(name='Alignment identitiy')

# etc.