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microdiversity.R
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microdiversity.R
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df$MeanDiSiperMbp <- df %>%
select(starts_with("DiSiperMbp")) %>%
as.matrix() %>%
rowMeans(na.rm = TRUE)
df$MeanNonsynonimousFraction <- df %>%
select(starts_with("NonsynonimousFraction")) %>%
as.matrix() %>%
rowMeans(na.rm = TRUE)
disi_array <- sapply(iter(filtered_df, by = "row"),
max_mapper, pattern = "DiSiperMbp")
nsf_array <- sapply(iter(filtered_df, by = "row"),
max_mapper, pattern = "NonsynonimousFraction")
tax_df <- filtered_df %>%
transmute(Tax = paste(Order, Family, gsub("metabat2bin_", "", genome), sep = ";"))
microdiversity_df <- data.frame("DiSiperMbpAtAbundMax" = disi_array,
"NonsynonimousFractionAtAbundMax" = nsf_array,
"AbundMax" = filtered_df$AbundMax,
"Tax" = tax_df$Tax) %>%
mutate(Tax = ifelse(NonsynonimousFractionAtAbundMax > 0.5, Tax, ""))
p <- ggplot(microdiversity_df, aes(x = DiSiperMbpAtAbundMax,
y = NonsynonimousFractionAtAbundMax,
colour = AbundMax)) +
geom_point(size = 1) +
geom_text_repel(aes(label = Tax),
size = 3,
colour = "red") +
labs(x = "Divergent Sites per Mbp at Max RPKM",
y = "Nonsynonymous Fraction at Max RPKM",
colour = "Max RPKM") +
theme_classic()
ggsave("microdiversity.pdf",
plot = p,
device = "pdf",
path = "results",
width = 10,
height = 7)