color within the ideogram || ancestry

[complexgenome]

hi there, thanks for this package.

This is really great. I'm interested to create graphics to display ancestry information, something like https://github.com/jordanlab/tagore

Is this something that can be achieved?

Thanks

[TickingClock1992]

Yes, of course. For example, you have three kinds of ancestry information types. Set three colors by colorset1 = c("#66c2a5", "#fc8d62", "#8da0cb"), and confer the three ancestry information types with values of "1", "2", and "3" in the overlaid file.

For example:

require(RIdeogram)

gene_density$Value <- sample(1:3, nrow(gene_density), replace = TRUE)
LTR_density$Value <- sample(1:3, nrow(gene_density), replace = TRUE)

ideogram(karyotype = human_karyotype, overlaid = gene_density, label = LTR_density, label_type = "heatmap", colorset1 = c("#66c2a5", "#fc8d62", "#8da0cb"), colorset2 = c("#66c2a5", "#fc8d62", "#8da0cb")) 
convertSVG("chromosome.svg", device = "png")

Then, you can get this:

If you have four types, then set four different colors and "1", "2", "3", and "4".

[liufy11]

en, I can create graphics to display ancestry information, but how to change the legend ? I want the legend to be one color for one ancestry type ,not in heatmap format.

[TickingClock1992]

Sorry, there is still no parameter for that in this version. I do suggest you modify the picture in AI or PS.

Best,

---

Zhaodong Hao

Key Laboratory of Forest Genetics and Biotechnology Ministry of Education of China College of Forestry Nanjing Forestry University Nanjing 210037 China

在 2020年11月5日，下午7:20，liufy11 notifications@github.com 写道：

en, I can create graphics to display ancestry information, but how to change the legend ? I want the legend to be one color for one ancestry type ,not in heatmap format.

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