Open mbuttner opened 1 year ago
I was using the harmony integration method in my pipeline and realized passing HVGs was not doing anything. Looking into the code, it's clear that the hvg argument is only used within the check_sanity function here and further in the check_hvg function here, which ultimately does not subset the input adata to keep only the hvgs:
def check_hvg(hvg, adata_var):
if type(hvg) is not list:
raise TypeError("HVG list is not a list")
else:
if not all(i in adata_var.index for i in hvg):
raise ValueError("Not all HVGs are in the adata object")
Hi there,
if I incorporate an HVG list in scanorama, the list is ignored and scanorama is run on all genes.
I defined an HVG list as follows (pancreatic islet dataset as example, downloaded from figshare):
Output:
e.g.
Here are my versions: