kelly-sovacool / mothur-sensspec-debug

mothur sens.spec()

library(here)
library(tidyverse)
set.seed(20211014)

dat <- read_tsv(here('results', 'sensspec_concat.tsv')) %>%
  mutate(paper = case_when(dataset == 'miseq_1.0_01' ~ 'Schloss_Cluster_PeerJ_2015',
                           dataset == 'mouse' ~ 'Sovacool_OptiFit_2021',
                           TRUE ~ 'unknown'),
         method = case_when(cluster_method == 'vdgc' ~ 'VSEARCH de novo',
                            cluster_method == 'cvsearch' ~ 'VSEARCH closed ref',
                            TRUE ~ 'unknown'))

## 
## ── Column specification ─────────────────────────────────────────────────────────────────────────────────
## cols(
##   .default = col_double(),
##   label...1 = col_character(),
##   label...15 = col_character(),
##   mothur_version = col_character(),
##   dataset = col_character(),
##   filetype = col_character(),
##   cluster_method = col_character(),
##   label = col_logical(),
##   label...16 = col_character()
## )
## ℹ Use `spec()` for the full column specifications.

dat %>%
  select(dataset, cluster_method, mothur_version, filetype, mcc, num_otus) %>%
  knitr::kable()

dataset	cluster_method	mothur_version	filetype	mcc	num_otus
miseq_1.0_01	vdgc	1.37.0	names	0.7772	1977
miseq_1.0_01	cvsearch	1.37.0	names	0.6935	864
miseq_1.0_01	vdgc	1.46.1	names	0.0000	1977
miseq_1.0_01	cvsearch	1.46.1	names	0.0000	864
miseq_1.0_01	vdgc	1.46.1	count_table	0.7772	1977
miseq_1.0_01	cvsearch	1.46.1	count_table	0.6947	864
mouse	vdgc	1.37.0	names	0.7762	2113
mouse	cvsearch	1.37.0	names	0.4991	870
mouse	vdgc	1.46.1	names	0.0000	2113
mouse	cvsearch	1.46.1	names	0.0000	870
mouse	vdgc	1.46.1	count_table	0.7762	2113
mouse	cvsearch	1.46.1	count_table	0.4991	870

dat %>% ggplot(aes(x=mothur_version, y=mcc, color=dataset, shape=filetype)) +
  geom_point(position = position_jitter(width=0.1, height = 0),
             size = 5, alpha=0.7) +
  facet_wrap("cluster_method") +
  ylim(0,1) +
  theme_bw()

dat %>% ggplot(aes(x=mothur_version, y=mcc, color=paper, shape=filetype)) +
  geom_point(position = position_jitter(width=0.1, height = 0),
             size = 5, alpha=0.7) +
  facet_wrap('method') +
  ylim(0,1) +
  theme_bw() +
  theme(legend.position = 'top',
        legend.title = element_blank())