导读

gggenes: Draw Gene Arrow Maps in 'ggplot2'。

Github：gggens
CRAN：gggenes: Draw Gene Arrow Maps in 'ggplot2'
Author：Introduction to ‘gggenes’

注意：
R version >= 3.6
gggenes依赖的ggfittext需要R 3.6以上，导致我用R 3.4.1安装gggenes失败。后来改用R 3.6.1成功安装。

Linux conda安装R 3.6：

# conda config --show  # 查看所有channel
conda install -c r r=3.6

一、输入数据

1. 基因组-基因-方向

library(ggplot2)
library(gggenes)
data(example_genes)
head(example_genes)

2. 基因组-基因-亚基因

head(example_subgenes)

二、画基因箭头图

1. 基础绘图

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")

2. 去掉背景

• theme_genes()

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") +
  theme_genes()

3. 按geneE对齐

• make_alignment_dummies()

dummies <- make_alignment_dummies(
  example_genes,
  aes(xmin = start, xmax = end, y = molecule, id = gene),
  on = "genE"
)

ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_blank(data = dummies) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

4. 设置箭头形状

• geom_gene_label()

ggplot(example_genes, 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") +
  geom_blank(data = dummies) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

5. 控制箭头方向

example_genes$direction <- ifelse(example_genes$strand == "forward", 1, -1)
ggplot(
  subset(example_genes, molecule == "Genome1"),
  aes(xmin = start, xmax = end, y = strand, fill = gene, forward = direction)
  ) +
  geom_gene_arrow() +
  theme_genes()

ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene, forward = direction)) +
    geom_gene_arrow() +
    facet_wrap(~ molecule, scales = "free", ncol = 1) +
    scale_fill_brewer(palette = "Set3") +
    theme_genes()

6. 标记亚基因位置

• geom_subgene_arrow()

ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule)) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  geom_gene_arrow(fill = "white") +
  geom_subgene_arrow(data = example_subgenes,
    aes(xmin = start, xmax = end, y = molecule, fill = gene,
        xsubmin = from, xsubmax = to), color="black", alpha=.7) +
  theme_genes()

7. 标记某基因组中某基因的亚基因位置

• geom_subgene_label()

ggplot(subset(example_genes, molecule == "Genome4" & gene == "genA"),
       aes(xmin = start, xmax = end, y = strand)
  ) +
  geom_gene_arrow() +
  geom_gene_label(aes(label = gene)) +
  geom_subgene_arrow(
    data = subset(example_subgenes, molecule == "Genome4" & gene == "genA"),
    aes(xsubmin = from, xsubmax = to, fill = subgene)
  ) +
  geom_subgene_label(
    data = subset(example_subgenes, molecule == "Genome4" & gene == "genA"),
    aes(xsubmin = from, xsubmax = to, label = subgene),
    min.size = 0
  )