2018-11-7 基因结构图绘制之gggenes
最重要的包参考链接补上
library(ggplot2)
# install.packages("gggenes")
# devtools::install_github("wilkox/gggenes")
library(gggenes)
p1 <- ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
geom_gene_arrow() +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
scale_fill_brewer(palette = "Set3")
ggsave("test.pdf", p, width = 10, height = 20)
image.png
注意这里绘图需要将Rstudio的绘图区拉到最高（尽量高，否则会报错）
- 为什么会知道了，参考了此链接
Error in grid.Call(C_convert, x, as.integer(whatfrom), as.integer(whatto), :
Viewport has zero dimension(s)
image.png
p2 <- ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end, y =molecule, fill = gene)) +
geom_gene_arrow() +
ggplot2::facet_wrap(~ molecule, scales = "free", ncol = 1) +
ggplot2::scale_fill_brewer(palette = "Set3") +
theme_genes()
dummies <- make_alignment_dummies(
example_genes,
ggplot2::aes(xmin = start, xmax = end, y = molecule, id = gene),
on = "genE"
)
image.png
geom_gene_arrow() +
ggplot2::geom_blank(data = dummies) +
ggplot2::facet_wrap(~ molecule, scales = "free", ncol = 1) +
ggplot2::scale_fill_brewer(palette = "Set3") +
theme_genes()
image.png
p4 <- ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end, y =molecule, fill = gene, label = gene)) +
geom_gene_arrow(arrowhead_height = unit(3, "mm"), arrowhead_width = unit(1, "mm")) +
geom_gene_label(align = "left") +
ggplot2::geom_blank(data = dummies) +
ggplot2::facet_wrap(~ molecule, scales = "free", ncol = 1) +
ggplot2::scale_fill_brewer(palette = "Set3") +
theme_genes()
image.png
example_genes$direction <- ifelse(example_genes$strand == "forward", 1, -1)
p5 <- ggplot2::ggplot(subset(example_genes, molecule == "Genome1"),
ggplot2::aes(xmin = start, xmax = end, y = strand, fill = gene,
forward = direction)) +
geom_gene_arrow() +
theme_genes()
image.png
