Using Color Lists

[Mall quis]

Hi,

I am having trouble with assigning color lists to heat maps. I know I can assign them in the data, but that is too much work. I want to use a list such as "spectral-9-div-rev" or a list created by myself and assign it to the heatmap.

I have read everything in your web, I have tried the tutorials, but when I run it, it says that the list of colors is not defined! 

If you can give some advice, I will appreciate it.

Thanks.

Regards,

Benjamin

[Martin Krzywinski]

To assign a list to a heatmap, just use it in place of a CSV list of colors.

So, instead of

color = spectral-9-div-9,spectral-9-div-8,spectral-9-div-7,...

use

color = spectral-9-div-rev

When Circos sees a color name that corresponds to a list (Brewer palette lists are defined in etc/colors.brewer.lists.conf), and if it expects a list (heatmap, stacked bar plot) it will interpret the list as if you've explicitly listed the colors.

The color assignment maps the min value of the heatmap to the first element in the list, and max to the last.

You can combine lists and colors. This gives you a white->red gradient, then black, then blue->white gradient for a total of 19 colors.

color = reds-9-seq,black,blues-9-seq-rev

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

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