/mothur-sensspec-debug

Primary LanguagePython

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())