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()
![](https://raw.githubusercontent.com/kelly-sovacool/mothur-sensspec-debug/main/figures/plot_mcc-1.png)
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())
![](https://raw.githubusercontent.com/kelly-sovacool/mothur-sensspec-debug/main/figures/for_lab_mtg-1.png)