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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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DoLouvainCluster: 'Not a graph object' #550

Open swbioinf opened 1 year ago

swbioinf commented 1 year ago

Calling doLouvainCluster yeilds the following error:

doLouvainCluster(go)

Error in igraph::as_data_frame(x = igraph_object, what = "edges") : Not a graph object

This seems to be due to a call of get_NearestNetwork within doLouvainCluster_community(), which does not return an igraph object (and also throws up a depreciation message).

igraph_object = get_NearestNetwork(gobject, nn_network_to_use = nn_network_to_use, network_name = network_name)

The following might work instead; igraph_object = getNearestNetwork(gobject, nn_network_to_use = nn_network_to_use, network_name = network_name, output="igraph")

Using Giotto_3.2

Thanks for a useful package!

RubD commented 1 year ago

HI @swbioinf

This should be fixed in the suite_dev branch (v3.2.1).

BenjaminDEMAILLE commented 1 year ago

Hi Giotto tema I got the same bug with Giotto 3.2 installed today