doLeidenSubCluster

[onahman]

It's a minor issue.
I am getting an error when running this function doLeidenSubCluster
Error in calculateHVG(gobject = new("giotto", raw_exprs = new("dgCMatrix", :
unused argument (difference_in_variance = 1)
seems like an easy fix.

Also, the usage example here:
https://rdrr.io/github/RubD/Giotto/man/doLeidenSubCluster.html
doLeidenSubCluster(gobject)
Doesn't work since it requires cluster_column to be specified.

[RubD]

Thanks for letting us know. I think this could actually be fixed by changing the defaults for the hvg_param parameter to:
hvg_param = list(reverse_log_scale = T, difference_in_cov = 1, expression_values = 'normalized')
I'll do more formal tests later this week.

We haven't found a good and simple way for the individual usage examples, but we're working on that for in the next version.