R语言gggenes包，基因组箭头图

R语言gggenes包，基因组箭头图

Snipaste_2021-05-24_08-24-03.png Snipaste_2021-05-24_08-24-41.png Snipaste_2021-05-24_08-26-17.png 双箭头线段图1.jpg

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

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")

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()
# Mon May 24 08:21:57 2021 --对齐
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()
# Mon May 24 08:24:59 2021 ----箭头形状--------------------------
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()
# Mon May 24 08:25:21 2021 ----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()
# Mon May 24 08:25:52 2021 --
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()
# Mon May 24 08:26:30 2021 ----标记亚基因位置--------------------------

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()
# Mon May 24 08:26:51 2021 --
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
  )
# Mon May 24 08:28:18 2021 -- end

# Mon May 24 08:29:17 2021 -

# 字符编码：UTF-8
# R 版本：R x64 4.1 for window 10
# cgh163email@163.com
# 个人笔记不负责任，拎了个梨🍐🍈
.rs.restartR()
require(ggplot2)
require(gggenes)
rm(list = ls());gc()

#随机数模拟坐标散点：
mydt1 <- data.frame(
  start = runif(100, 30, 35),
  end = runif(100, 30, 35) ,
  gene = sample(LETTERS[10:15], 100, replace =TRUE) ,
  molecule = sample(LETTERS[1:5], 100, replace =TRUE),
  strand  = sample(LETTERS[16:21], 100, replace =TRUE),
  co = substr(rainbow(100), 1, 7))
head(mydt1)# lat lon size type co
# Sun Jan 31 19:55:55 2021 --随机数模拟完毕

ggplot(mydt1,
       aes(xmin=start,
           xmax=end,
           y=molecule,
           fill=gene))+
  geom_gene_arrow() #  基础
# Mon May 24 08:36:03 2021 --
ggplot(mydt1,
       aes(xmin=start,
           xmax=end,
           y=molecule,
           fill=gene))+
  geom_gene_arrow()+
  scale_fill_brewer(palette = 'Set3')+ #  填色
  facet_wrap(scales = 'free',ncol = 1,~molecule) #  分组
# Mon May 24 08:40:19 2021 -----ex2-------------------------
dt <- mydt1[1:3,]
dt$molecule <- 'a'
dt$start <- c(1,3,5)
dt$end <- c(2,5,7)
ggplot(dt)+
  geom_gene_arrow(aes(xmin=start,
                      xmax=end,
                      y=molecule,
                      fill=gene))
# Mon May 24 08:45:02 2021 ----小段--------------------------
dt2 <- data.frame(
  molecule=rep('G4',5),
  gene=rep('gA',5),
  start=rep(0,5),
  end=rep(15,5),
  strand=rep('re',5),
  subgene=letters[1:5],
  from=c(2,5,7,7,9),
  to=c(4,6,9,9,12),
  or=rep(1,5),
  fx =rep(1,5)
)
dt2
ggplot(dt2,
         aes(xmin = start, xmax = end, y = strand)) +
  geom_gene_arrow() + #  总段
  geom_subgene_arrow(
    data =dt2,
    aes(
      xsubmin = from,
      xsubmax = to,
      fill = subgene
    )
  )
# Mon May 24 10:46:27 2021 --text
ggplot(dt2,
         aes(xmin = start, xmax = end, y = strand)) +
  geom_gene_arrow() + #  总段
  geom_subgene_arrow(
    data =dt2,
    aes(
      xsubmin = from,
      xsubmax = to,
      fill = subgene
    )
  )+

geom_subgene_label(
    data = dt2,
    aes(xsubmin = from, xsubmax = to, label = subgene),
    min.size = 0
  )
# Mon May 24 08:21:57 2021 --对齐
data(example_genes)
dummies <- make_alignment_dummies(
  example_genes,
  aes(xmin = start, xmax = end, y = molecule, id = gene),
  on = "genE"
)

# Mon May 24 08:24:59 2021 ----箭头形状--------------------------
ggplot(example_genes, aes(xmin = start, xmax = end, y =
                            molecule, fill = gene, label = gene)) +
  geom_gene_arrow(arrowhead_height = unit(3, "mm"), #  箭头高度
                  arrowhead_width = unit(10, "mm")) + #  箭头长度
  # geom_gene_label(align = "left") +
  # geom_blank(data = dummies) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  theme_genes()
# Mon May 24 10:55:58 2021 ----ex3--------------------------
ggplot(dt2,
       aes(xmin = 1, xmax = 14, y = strand)) +
  geom_gene_arrow(arrowhead_height = unit(3, "mm"), #  箭头高度
                  arrowhead_width = unit(10, "mm"), #  箭头长度
  # ,fill='#FFFFCC',
  color='#990033',
  aes( forward = -1))+#  总段
  geom_gene_arrow(arrowhead_height = unit(3, "mm"), #  箭头高度
                  arrowhead_width = unit(10, "mm"), #  箭头长度
  # fill='#FFFFCC',
  color='#990033',
  aes( forward = 1,
       xmin=2,xmax=15
       ))+#  总段

  geom_subgene_arrow(
    data =dt2,
    aes(
      xsubmin = from,
      xsubmax = to,
      fill = subgene
    ))+
  geom_subgene_label(
    data = dt2,
    aes(xsubmin = from, xsubmax = to, label = subgene),
    min.size = 0
  )+
  theme_genes()+ #  主题
  ggtitle(label = 'gg双箭头线段图')

ggsave(filename = '双箭头线段图1.jpg',dpi=300)