点图

GOinfo <- read_tsv("go.tb")
emapper <- read_tsv("pep.diamond.emapper.annotations", comment = "##") %>% rename(query = "#query")
# 读取时去掉`##`开头的行，而`#query`开头的行作为表头
GOannotation <- emapper %>%
  dplyr::select(GID = query, GO = GOs) %>%
  dplyr::filter(GO != "-") %>%
  separate_rows(GO, sep = ",") %>%
  left_join(GOinfo, by = "GO") %>%
  dplyr::select(-Description)
# genelist 赋值自己的基因集向量
enrich <- enricher(genelist,
                   TERM2GENE = GOannotation[c(2,1)],
                   TERM2NAME = GOinfo[1:2])
enrich2 <- as_tibble(enrich) %>%
  left_join(distinct(select(GOannotation, GO, level)), by = c("ID" = "GO")) %>%
  mutate(GeneRatio = as.numeric(str_replace(GeneRatio, "/.*", "")) / as.numeric(str_replace(GeneRatio, ".*/", ""))) %>%
  filter(!is.na(level)) %>%
  mutate(DescriptionLevel = str_c(Description, " | ", level))
DescriptionOrder <- enrich2 %>%
  arrange(desc(level), GeneRatio) %>%
  .$DescriptionLevel
# 排序
enrich2$DescriptionLevel <- factor(enrich2$DescriptionLevel, levels = DescriptionOrder)
p <- enrich2 %>%
  filter(GeneRatio > 0.03) %>%
  ggplot() +
  geom_point(aes(GeneRatio, DescriptionLevel, color = pvalue, size = -pvalue)) +
  scale_color_gradient(low = "red", high = "blue") +
  theme_bw()
pdf(gofile, width = 8, height = 9)
print(p)
dev.off()