if (FALSE) {
library(dplyr)
library(ggplot2)
library(wesanderson)
library(tidyr)
## histogram number of species per phylum
dat <- get_lab("sample_esu") %>%
dplyr::filter(phylum != "Metazoa") %>%
dplyr::group_by(phylum) %>%
dplyr::summarize(
n_esu = n_distinct(group_esu)
)
dat$phylum <- reorder(dat$phylum, dat$n_esu, sort)
pdf(file = "/tmp/diversity_histo.pdf", height = 5)
ggplot(dat, aes(x = phylum, y = n_esu)) +
geom_bar(stat = "identity", fill = wes_palette("Zissou")[1]) +
coord_flip() +
theme(axis.text = element_text(size = 12),
legend.text = element_text(size = 12),
axis.title = element_text(size = 12)) +
xlab("") + ylab("Number of species")
dev.off()
## histogram number of species that have a match per phylum
gg <- get_lab("sequencing_plate_data") %>%
filter(success == 1) %>%
filter(!is.na(bold_phylum_id)) %>%
group_by(bold_phylum_id) %>%
summarize(
n_spp = n_distinct(bold_species_id)
) %>%
ungroup %>%
rename(phylum = bold_phylum_id) %>%
right_join(dat)
gg$phylum <- reorder(gg$phylum, gg$n_esu, sort)
res <- gg %>%
gather(N, n_species, -phylum)
res$N <- factor(res$N, levels = c("n_spp", "n_esu"))
pal <- wes_palette("Zissou", 5)
svg(file = "~/Documents/2016-05-02.Whitney/percent_identified.svg", height = 5)
pdf(file = "/tmp/percent_identified.pdf", height = 5)
ggplot(res, aes(x = phylum, y = n_species, fill = N)) +
geom_bar(stat = "identity", position = "dodge") +
coord_flip() +
theme(axis.text = element_text(size = 12),
legend.text = element_text(size = 12),
axis.title = element_text(size = 12),
legend.position = "none") +
xlab("") + ylab("Number of species")
dev.off()
}
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