# Help

**URL:** https://discourse.scverse.org/c/help/27.md?page=5

[Latest](https://discourse.scverse.org/latest.md) · [Categories](https://discourse.scverse.org/categories.md) · [Tags](https://discourse.scverse.org/tags.md)

**Page:** 6

---

## [Mu.pp.intersect\_obs()](https://discourse.scverse.org/t/mu-pp-intersect-obs/3301)

<div class="topic-metadata">

**Author:** [@Drito](https://discourse.scverse.org/u/Drito)\
**Replies:** 7\
**Last updated:** [May 9, 2025, 4:04pm UTC](https://discourse.scverse.org/t/mu-pp-intersect-obs/3301 "2025-05-09T16:04:00Z")

</div>

Hello, I’m trying to integrate scATAC-seq and scRNA-seq from a 10x Genomics Multiome experiment, but I’m having problems when I run mu.pp.intersect\_obs(mdata). This is the error message: ValueError: Value passed for k…

---

## [Do multiple pairwise comparison with scCODA of pertpy](https://discourse.scverse.org/t/do-multiple-pairwise-comparison-with-sccoda-of-pertpy/3630)

<div class="topic-metadata">

**Author:** [@shihsama](https://discourse.scverse.org/u/shihsama)\
**Replies:** 3\
**Last updated:** [May 4, 2025, 10:02am UTC](https://discourse.scverse.org/t/do-multiple-pairwise-comparison-with-sccoda-of-pertpy/3630 "2025-05-04T10:02:38Z")

</div>

Hi, I’m using scCODA model to do composition analysis. As shown in tutorial, if we want to try different reference levels, just modify the treatment level in formula arguement. Now, if we got A,B,C and D four levels, an…

---

## [Nan values in the latent of scanvi\_query](https://discourse.scverse.org/t/nan-values-in-the-latent-of-scanvi-query/3619)

<div class="topic-metadata">

**Author:** [@mossishahi](https://discourse.scverse.org/u/mossishahi)\
**Replies:** 1\
**Last updated:** [April 23, 2025, 11:50am UTC](https://discourse.scverse.org/t/nan-values-in-the-latent-of-scanvi-query/3619 "2025-04-23T11:50:46Z")

</div>

Hi I’m trying to do a label transfer using SCANVI using the following script: import scanpy as sc import scvi # scvi==1.0.4 from scvi.model import SCVI from scvi.model import SCANVI import rapids\_singlecell as rsc pan…

---

## [Modify gene identifiers stored in existing scVI model](https://discourse.scverse.org/t/modify-gene-identifiers-stored-in-existing-scvi-model/3602)

<div class="topic-metadata">

**Author:** [@pcm32](https://discourse.scverse.org/u/pcm32)\
**Replies:** 1\
**Last updated:** [April 20, 2025, 1:59pm UTC](https://discourse.scverse.org/t/modify-gene-identifiers-stored-in-existing-scvi-model/3602 "2025-04-20T13:59:04Z")

</div>

Hi! I trained a lot of scVI models with different parameters to asses their impact, however I realised at the end of the exercise that the original AnnData file was indexed in var through a simple numeric index (so the i…

---

## [Anndata Manager Store](https://discourse.scverse.org/t/anndata-manager-store/3594)

<div class="topic-metadata">

**Author:** [@Mariano](https://discourse.scverse.org/u/Mariano)\
**Replies:** 11\
**Last updated:** [April 20, 2025, 7:52am UTC](https://discourse.scverse.org/t/anndata-manager-store/3594 "2025-04-20T07:52:04Z")

</div>

Hi, I have a basic question about the procedure to run scvi models. When a model is created and trained, we run 3 instructions, 1) setup\_anndata, 2) instantiate the model, 3) model.train() My understanding is that when…

---

## [Scvi package can't be installed into google colab?](https://discourse.scverse.org/t/scvi-package-cant-be-installed-into-google-colab/3600)

<div class="topic-metadata">

**Author:** [@Jihua-Liu](https://discourse.scverse.org/u/Jihua-Liu)\
**Replies:** 6\
**Last updated:** [April 20, 2025, 7:17am UTC](https://discourse.scverse.org/t/scvi-package-cant-be-installed-into-google-colab/3600 "2025-04-20T07:17:49Z")

</div>

It was working two weeks ago, but now it just doesn’t work.

---

## [How to retreive the V,D,J gene segment idenifiers and CD3 sequence give a clone\_id?](https://discourse.scverse.org/t/how-to-retreive-the-v-d-j-gene-segment-idenifiers-and-cd3-sequence-give-a-clone-id/3609)

<div class="topic-metadata">

**Author:** [@lesande](https://discourse.scverse.org/u/lesande)\
**Replies:** 1\
**Last updated:** [April 18, 2025, 11:59am UTC](https://discourse.scverse.org/t/how-to-retreive-the-v-d-j-gene-segment-idenifiers-and-cd3-sequence-give-a-clone-id/3609 "2025-04-18T11:59:01Z")

</div>

I have mdata which has ‘gex’ and ‘airr’ slots (the mdata structure is below). Then I did: ir.pp.ir\_dist(mdata) ir.tl.define\_clonotypes(mdata, receptor\_arms="all", dual\_ir="primary\_only") Which ran successfully. I see …

---

## [Is the scVI model applicable to bulk RNA-seq data from cell lines?](https://discourse.scverse.org/t/is-the-scvi-model-applicable-to-bulk-rna-seq-data-from-cell-lines/3610)

<div class="topic-metadata">

**Author:** [@Yao](https://discourse.scverse.org/u/Yao)\
**Replies:** 1\
**Last updated:** [April 16, 2025, 5:27am UTC](https://discourse.scverse.org/t/is-the-scvi-model-applicable-to-bulk-rna-seq-data-from-cell-lines/3610 "2025-04-16T05:27:00Z")

</div>

Hi guys, I know that scVI is primarily designed for modeling UMI-based single-cell RNA-seq counts, but I’m wondering whether it might also be applicable to bulk RNA-seq data from homogeneous cell lines. Since bulk RNA-s…

---

## [Best Practices for Multi-Panel Figures](https://discourse.scverse.org/t/best-practices-for-multi-panel-figures/3603)

<div class="topic-metadata">

**Author:** [@wbrett87](https://discourse.scverse.org/u/wbrett87)\
**Replies:** 0\
**Last updated:** [April 11, 2025, 8:43pm UTC](https://discourse.scverse.org/t/best-practices-for-multi-panel-figures/3603 "2025-04-11T20:43:25Z")

</div>

Hello everyone, I am putting together a multi-panel figure containing bioinformatic plots from that are getting output from a variety of different python scRNAseq packages. One problem I am encountering is that when I u…

---

## [How to transfer annotation from cell subset to original object?](https://discourse.scverse.org/t/how-to-transfer-annotation-from-cell-subset-to-original-object/3494)

<div class="topic-metadata">

**Author:** [@maisom](https://discourse.scverse.org/u/maisom)\
**Replies:** 1\
**Last updated:** [April 10, 2025, 9:29pm UTC](https://discourse.scverse.org/t/how-to-transfer-annotation-from-cell-subset-to-original-object/3494 "2025-04-10T21:29:05Z")

</div>

Hi, I can not find an answer to this anywhere, so I create a post, hope you can help me. I am a beginner in bioinformatics and single cell analysis. I have a large dataset of immune cells from two types of tissues tha…

---

## [How to plot annotation in Xenium data using spatialdata](https://discourse.scverse.org/t/how-to-plot-annotation-in-xenium-data-using-spatialdata/3468)

<div class="topic-metadata">

**Author:** [@christophechu](https://discourse.scverse.org/u/christophechu)\
**Replies:** 8\
**Last updated:** [April 10, 2025, 9:24pm UTC](https://discourse.scverse.org/t/how-to-plot-annotation-in-xenium-data-using-spatialdata/3468 "2025-04-10T21:24:39Z")

</div>

sdata.pl.render\_shapes('cell\_boundaries', color='leiden', cmap='Set3').pl.show() there is no annotation be plotted.

---

## [How should I calculate the knn entropy using the leiden clusters?](https://discourse.scverse.org/t/how-should-i-calculate-the-knn-entropy-using-the-leiden-clusters/3537)

<div class="topic-metadata">

**Author:** [@danli349](https://discourse.scverse.org/u/danli349)\
**Replies:** 1\
**Last updated:** [April 10, 2025, 7:55am UTC](https://discourse.scverse.org/t/how-should-i-calculate-the-knn-entropy-using-the-leiden-clusters/3537 "2025-04-10T07:55:39Z")

</div>

Hello: How should I calculate the knn entropy using the leiden clusters? https://arxiv.org/pdf/1506.06501v1 Thanks a lot

---

## [Understanding scVI integration inside R with Seurat v5 & SCTransform](https://discourse.scverse.org/t/understanding-scvi-integration-inside-r-with-seurat-v5-sctransform/3588)

<div class="topic-metadata">

**Author:** [@y.grabovska](https://discourse.scverse.org/u/y.grabovska)\
**Replies:** 1\
**Last updated:** [April 6, 2025, 8:52am UTC](https://discourse.scverse.org/t/understanding-scvi-integration-inside-r-with-seurat-v5-sctransform/3588 "2025-04-06T08:52:48Z")

</div>

I have a set of single-cell libraries from an drug treatment experiment - early timepoint, treatment/DMSO at 3 timepoints (21 libraries total). I have preprocessed each library separately with Seurat using SCTransform v…

---

## [How to fix number of nodes used in HPC environment with scvi.train (via R & reticulate)?](https://discourse.scverse.org/t/how-to-fix-number-of-nodes-used-in-hpc-environment-with-scvi-train-via-r-reticulate/3579)

<div class="topic-metadata">

**Author:** [@ZheFrench](https://discourse.scverse.org/u/ZheFrench)\
**Replies:** 8\
**Last updated:** [April 10, 2025, 6:01am UTC](https://discourse.scverse.org/t/how-to-fix-number-of-nodes-used-in-hpc-environment-with-scvi-train-via-r-reticulate/3579 "2025-04-10T06:01:55Z")

</div>

Hi, I’m using scvi via R using reticulate. All cpu nodes of the clusters are used, I would like to restrain this behavior when I call model$train function. Also I wanted to know if I should start the integration from …

---

## [Stacked violin API related question](https://discourse.scverse.org/t/stacked-violin-api-related-question/545)

<div class="topic-metadata">

**Author:** [@khksw0403](https://discourse.scverse.org/u/khksw0403)\
**Replies:** 2\
**Last updated:** [April 1, 2025, 9:11pm UTC](https://discourse.scverse.org/t/stacked-violin-api-related-question/545 "2025-04-01T21:11:06Z")

</div>

Good morning, now i use scanpy module and get results. but when i use \[name.add\_totals()\] function, i don’t know how to save it pdf or image files. sample1: → it’s working sc.pl.stacked\_violin(data, markers, groupby=‘s…

---

## [Any MLX (MPS) framework accelerate solution for scanpy？](https://discourse.scverse.org/t/any-mlx-mps-framework-accelerate-solution-for-scanpy/3452)

<div class="topic-metadata">

**Author:** [@c0nleyinnnn](https://discourse.scverse.org/u/c0nleyinnnn)\
**Replies:** 1\
**Last updated:** [March 31, 2025, 3:53pm UTC](https://discourse.scverse.org/t/any-mlx-mps-framework-accelerate-solution-for-scanpy/3452 "2025-03-31T15:53:59Z")

</div>

On the NVIDIA platform, the rapids-singlecell library uses CUDA to achieve very fast single-cell data processing and calculation. The unified memory architecture of the M chip is very beneficial for single-cell data anal…

---

## [Getting the same values to have the same colors across multiple plots of spatial\_segment?](https://discourse.scverse.org/t/getting-the-same-values-to-have-the-same-colors-across-multiple-plots-of-spatial-segment/3568)

<div class="topic-metadata">

**Author:** [@YonSa](https://discourse.scverse.org/u/YonSa)\
**Replies:** 0\
**Last updated:** [March 24, 2025, 1:36pm UTC](https://discourse.scverse.org/t/getting-the-same-values-to-have-the-same-colors-across-multiple-plots-of-spatial-segment/3568 "2025-03-24T13:36:48Z")

</div>

I’m calling: sq.pl.spatial\_segment( fov, color=\['method\_1', 'method\_2'\], library\_key="fov", library\_id=fov\_num, seg\_cell\_id="cell\_ID", title=f"{method}, FOV {fov\_num} …

---

## [inferCNVpy after running scVI with batch as key](https://discourse.scverse.org/t/infercnvpy-after-running-scvi-with-batch-as-key/848)

<div class="topic-metadata">

**Author:** [@zvittorio](https://discourse.scverse.org/u/zvittorio)\
**Replies:** 5\
**Last updated:** [March 24, 2025, 7:19am UTC](https://discourse.scverse.org/t/infercnvpy-after-running-scvi-with-batch-as-key/848 "2025-03-24T07:19:32Z")

</div>

Hi scverse community, I have at my disposal a bunch of datasets, of which one is a cancer patient while the other ones are the same organ but in a healthy condition. The idea is to use the cell types of the healthy sam…

---

## [Suggestions for training on xenium spatial transcriptomics dataset](https://discourse.scverse.org/t/suggestions-for-training-on-xenium-spatial-transcriptomics-dataset/3394)

<div class="topic-metadata">

**Author:** [@abs51295](https://discourse.scverse.org/u/abs51295)\
**Replies:** 5\
**Last updated:** [March 22, 2025, 7:51pm UTC](https://discourse.scverse.org/t/suggestions-for-training-on-xenium-spatial-transcriptomics-dataset/3394 "2025-03-22T19:51:20Z")

</div>

Hey @cane11 , We have been using baysor followed by scVI so far for batch correction on Xenium datasets. It’s working fine out of the box where it’s able to discern major cell populations. One problem we see frequently …

---

## [How to generate continuous colormap to plot the (co-)expression of multiple genes](https://discourse.scverse.org/t/how-to-generate-continuous-colormap-to-plot-the-co-expression-of-multiple-genes/3563)

<div class="topic-metadata">

**Author:** [@LioLnr](https://discourse.scverse.org/u/LioLnr)\
**Replies:** 0\
**Last updated:** [March 20, 2025, 12:54pm UTC](https://discourse.scverse.org/t/how-to-generate-continuous-colormap-to-plot-the-co-expression-of-multiple-genes/3563 "2025-03-20T12:54:25Z")

</div>

I would like to generate a figure like this. Does anyone have an idea how I could do ? Best regards

---

## [Error when running scvi.data.add\_dna\_sequence](https://discourse.scverse.org/t/error-when-running-scvi-data-add-dna-sequence/3549)

<div class="topic-metadata">

**Author:** [@afarha5](https://discourse.scverse.org/u/afarha5)\
**Replies:** 1\
**Last updated:** [March 18, 2025, 8:08am UTC](https://discourse.scverse.org/t/error-when-running-scvi-data-add-dna-sequence/3549 "2025-03-18T08:08:00Z")

</div>

Hello, I am getting an error when running simple commands like: import genomepy # Define genome directory genome\_dir = "data" # Install mm10 genomepy.install\_genome("mm10",provider="ensembl", genomes\_dir=genome\_dir) …

---

## [Scvi-tools solo return synthetic doublets](https://discourse.scverse.org/t/scvi-tools-solo-return-synthetic-doublets/3545)

<div class="topic-metadata">

**Author:** [@v3ritatis](https://discourse.scverse.org/u/v3ritatis)\
**Replies:** 3\
**Last updated:** [March 18, 2025, 8:55pm UTC](https://discourse.scverse.org/t/scvi-tools-solo-return-synthetic-doublets/3545 "2025-03-18T20:55:02Z")

</div>

Is it possible to return the synthetic doublets with solo. I would like to be able to run pca on my adata with the synthetic doublets and visualize what my cell clusters look like relative to the stimulated doublets.

---

## [SysVI model and normalized expression](https://discourse.scverse.org/t/sysvi-model-and-normalized-expression/3543)

<div class="topic-metadata">

**Author:** [@danieljrichard](https://discourse.scverse.org/u/danieljrichard)\
**Replies:** 1\
**Last updated:** [March 15, 2025, 7:32am UTC](https://discourse.scverse.org/t/sysvi-model-and-normalized-expression/3543 "2025-03-15T07:32:36Z")

</div>

Hello, I was working through this example for running SysVI: And tried running get\_normalized expression. However, I get this error: AttributeError: ‘SysVI’ object has no attribute ‘get\_normalized\_expression’ Howeve…

---

## [Scvi-tools and xenium](https://discourse.scverse.org/t/scvi-tools-and-xenium/2450)

<div class="topic-metadata">

**Author:** [@wangjiawen2013](https://discourse.scverse.org/u/wangjiawen2013)\
**Replies:** 7\
**Last updated:** [March 13, 2025, 5:58pm UTC](https://discourse.scverse.org/t/scvi-tools-and-xenium/2450 "2025-03-13T17:58:30Z")

</div>

Hi, Can I use scvi-tools to process 10x genomics xenium spatial transcriptome dataset ? The following adata is an anndata object from xenium dataset. # Registering the data scvi.model.SCVI.setup\_anndata(adata, layer="c…

---

## [Unexpected exception formatting exception when prepare\_query\_anndata](https://discourse.scverse.org/t/unexpected-exception-formatting-exception-when-prepare-query-anndata/3533)

<div class="topic-metadata">

**Author:** [@SherylShaw](https://discourse.scverse.org/u/SherylShaw)\
**Replies:** 4\
**Last updated:** [March 11, 2025, 1:45pm UTC](https://discourse.scverse.org/t/unexpected-exception-formatting-exception-when-prepare-query-anndata/3533 "2025-03-11T13:45:51Z")

</div>

Hello, thanks for the tool! I’m trying to do the label transfer from a ref data to my query data. I’m following this turorial: Human Endometrial Cell Atlas (HECA): a step-by-step guide to mapping query endometrial data…

---

## [DestVI: how to load a DestVI model that was saved as a pickle](https://discourse.scverse.org/t/destvi-how-to-load-a-destvi-model-that-was-saved-as-a-pickle/3530)

<div class="topic-metadata">

**Author:** [@jliu678](https://discourse.scverse.org/u/jliu678)\
**Replies:** 1\
**Last updated:** [March 9, 2025, 1:44pm UTC](https://discourse.scverse.org/t/destvi-how-to-load-a-destvi-model-that-was-saved-as-a-pickle/3530 "2025-03-09T13:44:59Z")

</div>

Hi scvi team, DestVI model was saved as a pickle as below: DestVI.setup\_anndata(st\_adata, layer="counts") st\_model = DestVI.from\_rna\_model(st\_adata, sc\_model) st\_model.view\_anndata\_setup() st\_model.train(max\_epochs=250…

---

## [Parameters in training model for integrating datasets with scVI in R](https://discourse.scverse.org/t/parameters-in-training-model-for-integrating-datasets-with-scvi-in-r/3522)

<div class="topic-metadata">

**Author:** [@joweihsieh](https://discourse.scverse.org/u/joweihsieh)\
**Replies:** 13\
**Last updated:** [March 9, 2025, 12:36pm UTC](https://discourse.scverse.org/t/parameters-in-training-model-for-integrating-datasets-with-scvi-in-r/3522 "2025-03-09T12:36:23Z")

</div>

Thanks for developing this tool!! I was trying to use scVI to integrate my datasets. Following the instructions (Integrating datasets with scVI in R — scvi-tools), I was able to run the script successfully without chang…

---

## [Understanding batch-corrected counts in scVI](https://discourse.scverse.org/t/understanding-batch-corrected-counts-in-scvi/3526)

<div class="topic-metadata">

**Author:** [@noraneko](https://discourse.scverse.org/u/noraneko)\
**Replies:** 6\
**Last updated:** [March 9, 2025, 12:39am UTC](https://discourse.scverse.org/t/understanding-batch-corrected-counts-in-scvi/3526 "2025-03-09T00:39:13Z")

</div>

Hi, Thank you for such a great tool! I’m analyzing transcriptional heterogeneity in a single cell type associated with a condition of interest. I have multiple scRNA-seq datasets, each containing samples from both cond…

---

## [Add new data to existing integration](https://discourse.scverse.org/t/add-new-data-to-existing-integration/3495)

<div class="topic-metadata">

**Author:** [@tangxj](https://discourse.scverse.org/u/tangxj)\
**Replies:** 3\
**Last updated:** [March 7, 2025, 8:04am UTC](https://discourse.scverse.org/t/add-new-data-to-existing-integration/3495 "2025-03-07T08:04:27Z")

</div>

Hi all, I have a large integrated adata (~4M cells) through SCVI (with 2K HVG) and now I am going to add a small new single-cell data (28K cells) into the large integration. Is there a quick way to “project” the large i…

---

## [Split dotplot by condition](https://discourse.scverse.org/t/split-dotplot-by-condition/2513)

<div class="topic-metadata">

**Author:** [@spatts14](https://discourse.scverse.org/u/spatts14)\
**Replies:** 2\
**Last updated:** [March 3, 2025, 4:53pm UTC](https://discourse.scverse.org/t/split-dotplot-by-condition/2513 "2025-03-03T16:53:58Z")

</div>

Is possible to do something like this in scanpy? (see photo below) It would be great if it could be seperated by cell type, gene, and condition like x axis (bottom) = gene x axis (top) = condition (i.e one column f…

[Previous page](https://discourse.scverse.org/c/help/27.md?page=4)

[Next page](https://discourse.scverse.org/c/help/27.md?page=6)