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jokergoo / ComplexHeatmap

Make Complex Heatmaps
https://jokergoo.github.io/ComplexHeatmap-reference/book/
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Error: C stack usage 7971584 is too close to the limit #972

Closed gorliver closed 2 years ago

gorliver commented 2 years ago

Hi, Thank you for the great tool. I've been using it for a long time and recently have this error when plotting a large matrix(40000 x 80):

Error: C stack usage  7971584 is too close to the limit

I use the latest github version.

Thank you!

gorliver commented 2 years ago

I can share my matrix in any way that is convenient for you.

jokergoo commented 2 years ago

Maybe you can put the matrix in google drive and then share it with me?

gorliver commented 2 years ago

Here is the file: https://drive.google.com/file/d/1_fk_kqv_xL5QGfLbwyC97uf5ktKRONqJ/view?usp=sharing

I figured the error is from dendsort. Can you recommend other tools for sorting dendrogram?

jokergoo commented 2 years ago

Maybe dendsort does not support reordering such a big dendrogram.

There may be two other options:

  1. use the reorder.dendrogram() in stats package. This is also used in ComplexHeatmap.
  2. use the seriation package. It provides many methods to directly reorder the matrix.
gorliver commented 2 years ago

Thank you for the recommendation. I'm closing the issue!