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TickingClock1992 / RIdeogram

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How to set the midpoint of colour #4

Closed QianzhaoJ closed 4 years ago

QianzhaoJ commented 5 years ago

Hi: So useful package this is ! However, I have some annotion data like ：

1 3000500 3136999 -0.338434787450111
1 37321500 37489499 -0.533675006500781
1 37510500 37673999 -0.567659305780682
1 49247000 49471999 -0.781532436705488
1 153160500 153286999 -0.275541774503734

The range of fourth column is -0.9,0.5 ,and I want to set 0 as the midpoint of colours，Ideogram seems to set the mean as the midpoint of colours.
Could you give me some advice ? Thanks in advance !

TickingClock1992 commented 5 years ago

Sorry for some delay with response. Now, Ideogram set the mean as the midpoint of color. We are planning to add the function that users can set the value for the midpoint color. However, there is still an alternative way you can do this. "0" is about the two-thirds. You can write the code like this: ideogram(karyotype = human_karyotype, overlaid = gene_density, colorset1 = c("#d7191c", "#fdae61", "#ffffbf", "#2c7bb6")) Then, you can get a picture set the two-thirds value as the midpoint color. chromosome

pengbo233 commented 5 years ago

你好！ 请问下，图例的low high是否可以设置为我自己想要设置的数字，从脚本提供信息来看，只有移动legend,而没有设置上下限具体数值的参数 祝好！

pengbo233 commented 5 years ago

想到了，可以直接修改SVG，嗯，谢谢

Frankshi5011 commented 5 years ago

Hello, This is a great tool. Can I draw the ideogram for mouse cells? It seems that there is no mouse karyotype data in the package?

Thanks

Frank

TickingClock1992 commented 5 years ago

Hello, This is a great tool. Can I draw the ideogram for mouse cells? It seems that there is no mouse karyotype data in the package?

Thanks

Frank

Hi, you can make your own ideogram file very easily in .TXT format and then read it as a data frame with the function read.table. Happy Drawing!

Frankshi5011 commented 4 years ago

Thanks so much! Huidong

Sent from my iPhone

On Sep 9, 2019, at 3:20 AM, Zhaodong Hao notifications@github.com wrote:

Hello, This is a great tool. Can I draw the ideogram for mouse cells? It seems that there is no mouse karyotype data in the package?

Thanks

Frank

Hi, you can make your own ideogram file very easily in .TXT format and then read it as a data frame with the function read.table. Happy Drawing!

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