❝小编很久之前写过一系列基因家族数据可视化的文档，最近对基因家族数据可视化又有了新的认识下面来绘制这一类文章里面的一张常用图，下面来看具体操作 ❞
绘制进化树
代码语言：javascript复制tree <- read.newick("tree.nwk",node.label = "support") %>%
ggtree(branch.length = "none")
theme_void()
theme(legend.title=element_blank(),
legend.position = c(0.1,1.2), legend.justification = c(0,1.2),
legend.text=element_text(color="black",size=8))
绘制蛋白保守结构域
代码语言：javascript复制pfam <- read_tsv("pfam.xls",col_names = F) %>%
select(1,4,5,6,12) %>%
filter(X12 < 0.001) %>%
mutate_at(vars("X5"),~str_split(.,"\.",simplify=TRUE)[,1]) %>%
separate(`X5`,into=c("A","B"),sep="-") %>%
mutate(A=as.numeric(A)) %>%
select(-X12,-B) %>%
set_colnames(c("gene","start","end","hmm_acc")) %>%
ggplot(aes(xmin = start,xmax = end,y=gene,fill = hmm_acc))
geom_gene_arrow(arrowhead_height = unit(0, "mm"),
arrowhead_width = unit(0,"mm"))
labs(y=NULL)
theme(
axis.text.y=element_blank(),
axis.text.x=element_text(color="black"),
legend.title = element_blank(),
legend.spacing.x=unit(0.1,'cm'),
legend.key.width=unit(0.4,'cm'),
legend.position = "top",
legend.text=element_text(color="black",size=8),
legend.key.height=unit(0.4,'cm'),
plot.margin=unit(c(0,0,0,0),units="cm"))
guides(fill = guide_legend(direction = "horizontal"))
guides(fill=guide_legend(nrow=1, byrow=TRUE))
绘制基因结构图
代码语言：javascript复制gene <- gggenomes("A.gff")
geom_gene(position="pile",size=3)
theme(plot.margin=unit(c(1.1,0,0,0),units="cm"))
拼图
代码语言：javascript复制g <- gene %>% pick_by_tree(tree) %>% ggplotify::as.grob() %>% ggdraw()
pp <- tree pfam plot_layout(widths = c(.6,1))
(pp %>% ggdraw()|g) theme(plot.margin=unit(c(0,0,0,0),units="cm"))
