染色体上画基因结构图分布图之gggenes

2018-11-7 基因结构图绘制之gggenes

最重要的包参考链接补上

• https://github.com/wilkox/gggenes

• 安装包

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