kaarg2

> Here's a minimal example of the bug I run into: > > ```python > import scanpy as sc > import anndata > print("scanpy", sc.__version__) # 1.9.3 > print("anndata", anndata.__version__)...

There might be some entries in adata.obs or the title of some obs column contain illegal character such as "/". You can try changing those characters in your adata.obs. Alternatively,...

Have you tried running as.data.frame before running superheat? df On Oct 6, 2018, at 8:18 PM, Frederica1 wrote: > > For a start I'm trying to plot a simple heatmap....

To include only numeric data, you can use the as.matrix function. df On Oct 6, 2018, at 8:18 PM, Frederica1 wrote: > > For a start I'm trying to plot...

I think you also need to construct a separate vector for the labels, in case you want to color code the label. When you import the data, did you check...

You might want to specify the row names and headers when you import the data. df On Oct 6, 2018, at 10:21 PM, Frederica1 wrote: > > I'm sure it's...

I don’t think the function you described draw a heat map. You might want to refer to the example below. https://rlbarter.github.io/superheat-examples/Organ/ Yun Zhang (Alex) > On Oct 6, 2018, at...

You can try remove the site column but preserve the sample ID. then color code the sample based on the site. Treating site as a factor variable. You will need...