RIdeogram绘制基因组染色体标记图

Y叔团队参与开发的一个R包RIdeogram，可用来绘制基因组染色体的可视化图形，如基因密度、分子标记等。

直接上代码。

#install.packages("RIdeogram")
library(RIdeogram)
data(human_karyotype, package="RIdeogram")
data(gene_density, package="RIdeogram")
data(Random_RNAs_500, package="RIdeogram")

数据格式：

> head(human_karyotype)
  Chr Start       End  CE_start    CE_end
   1     0 248956422 122026459 124932724
   2     0 242193529  92188145  94090557
   3     0 198295559  90772458  93655574
   4     0 190214555  49712061  51743951
   5     0 181538259  46485900  50059807
   6     0 170805979  58553888  59829934
   
> head(gene_density)
  Chr   Start     End Value
   1       1 1000000    65
   1 1000001 2000000    76
   1 2000001 3000000    35
   1 3000001 4000000    30
   1 4000001 5000000    10
   1 5000001 6000000    10

> head(Random_RNAs_500)
   Type    Shape Chr    Start      End  color
  tRNA   circle   6 69204486 69204568 6a3d9a
  rRNA      box   3 68882967 68883091 33a02c
  rRNA      box   5 55777469 55777587 33a02c
  rRNA      box  21 25202207 25202315 33a02c
 miRNA triangle   1 86357632 86357687 ff7f00
 miRNA triangle  11 74399237 74399333 ff7f00

绘图。

ideogram(karyotype = human_karyotype)
convertSVG("chromosome.svg", device = "png")

ideogram(karyotype = human_karyotype, overlaid = gene_density)
convertSVG("chromosome.svg", device = "png")

ideogram(karyotype = human_karyotype, 
         overlaid = gene_density,
         label = Random_RNAs_500, 
         label_type = "marker")
convertSVG("chromosome.svg", device = "png")

更多细节可查看：https://cran.r-project.org/web/packages/RIdeogram/vignettes/RIdeogram.html

注意事项：输入数据的列名需与示例数据一致。