setwd('~/code/transrate-paper/analysis/score-testing/')
df <- read.csv('trinity-Osativa_204_protein.fa_Trinity.fasta_contigs.csv', as.is=T)

Contig score distribution

## Warning: Removed 2258 rows containing non-finite values (stat_density).

plot of chunk unnamed-chunk-2

Score component correlation

## Warning: the standard deviation is zero
## Warning: the standard deviation is zero
## Warning: the standard deviation is zero
## Warning: the standard deviation is zero

plot of chunk unnamed-chunk-3

Distribution of score components

## Warning: Removed 53 rows containing non-finite values (stat_density).
## Warning: Removed 2258 rows containing non-finite values (stat_density).
## Warning: Removed 53 rows containing non-finite values (stat_density).
## Warning: Removed 1053 rows containing non-finite values (stat_density).

plot of chunk unnamed-chunk-4

Correlation between score components

note: in this assembly, p_unambiguous is always 1 because Trinity replaces unambiguous bases.

## Warning: the standard deviation is zero
## Warning: Removed 8 rows containing missing values (geom_text).

plot of chunk unnamed-chunk-5