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Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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error when running celltree_maptpx #127

Open ch8316f5eyu opened 2 years ago

ch8316f5eyu commented 2 years ago

Hi, when I run the method of "celltree_maptpx", there is an error that indicates no expression associated with dataset. But I already add it by wrap_expression but is OK for other methods. How to solve it?

Dataset <- wrap_expression(counts = GetAssayData(seurat, 'count') %>% t, expression = GetAssayData(seruat, 'data') %>% t)  
model <- infer_trajectory(Dataset, 'celltree_maptpx')

The error message is:

Running singularity exec 'docker://dynverse/ti_celltree_maptpx:v0.9.9.01' echo hi
Running /home/weiyu/bin/singularity exec --containall -B '/tmp/RtmpfBXKaM/filef37e14557db6a/:/copy_mount,/tmp/RtmpfBXKaM/filef37e13ceec23d/tmp:/tmp2' 'docker://dynverse/ti_celltree_maptpx:v0.9.9.01' cp /code/definition.yml /copy_mount/
INFO:    Using cached SIF image
INFO:    Converting SIF file to temporary sandbox...
INFO:    Cleaning up image...
Error in get_expression(dataset, expression_source) :
  No expression found in trajectory, please provide the expression through the expression_source argument. This can be an expression or counts matrix, or a dataset containing the expression.

And it didn't work even I add "parameters = list('expression_source' = get_expression(Dataset, 'counts')" inside the function infer_trajectory