New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Using Monocle 3 with Seurat 3 integrated object #1658
Comments
Additional follow-up question: should I be using the batch-corrected, integrated gene values in the "integrated" assay or the non-integrated gene values in the "RNA" assay for downstream Monocle analyses? |
@dwucsf I have the same question as you.And from one user's post,the code showed integrated assay.But i also want to know if it's OK,because satijalab said that Seurat does not return batch-corrected expression values. Instead, Seurat can be used to generate a corrected cell/cell distance matrix. |
I'm able to run Monocle 3 with Seurat 3's integrated cells/counts, but I'm trying to construct my CDS in such a way that it contains original RNA count and integrated count data. I haven't figured this out. Have you? |
Hi @dwucsf, Seurat has support for the Monocle v2 object. However, we don't have support for Monocle v3 as it's still under development. Once Monocle v3 has been finalized and the object is no longer in development, we will work on adding support for the v3 Monocle v2 support is present in the development version of Seurat. To install the development version of Seurat, please see the instructions here. |
@mojaveazure Hi, |
Just to echo what @Sophia409 has stated: If it's simple to make a Monocle v3 CellDataSet contain two assays (i.e. be able to hold both integrated counts and original RNA counts) instead of being single-assay, that would be extremely helpful! Thank you!! |
Or, if you have other suggestions on how to approach this problem, I am more than happy to hear your suggestions! |
@Sophia409 and @dwucsf, Monocle v3 is in beta and under active development. We are working on adding support for Monocle v3, but are unable to provide more details at this time. Moreover, in order for us to be able to release new versions of Seurat on CRAN, we can only depend on packages on CRAN, Bioconductor, or another CRAN-like repository. Monocle v3 is not yet on a repository, only GitHub, and as we have other improvements to Seurat in the pipeline, we want the flexibility to release on our schedule. Rest assured, once Monocle v3 is fully released, we will build support for the v3 |
following this thread! Thank you for the clarification |
Final_Seurat_to_Monocle3_2D_and_3D_190719 2.txt |
This script is great! Thank you for posting. The one step that gave me issues was the "Assign cluster info" step. Any advice for me if I get the warning "object 'list_cluster' not found" and "object 'cluster.res' not found"? |
@zihengxuwu Hello,your script imported the RNA counts not the integrated data.But I have to use the batch integrated data of Seurat.In addition, monocle3 is not the final edition,and its result trajectory is really not available for me.So I still use monocle 2 to do it. |
@mojaveazure Hello,I have a question.You said that Monocle v2 support is present in the development version of Seurat.So it means that we can convert seurat v3 object to monocle 2 celldataSet object through the development version?Is there any tutorial about how to make this conversion in this version?I couldn't find it. |
@Sophia409 @dwucsf did any of you guys figure out how to create a pseudotime plot with integrated seurat object calculations yet plot expression data on them using expression values from either the SCT DATA or RNA DATA slots? I am also having the same problem, and feel like there has to be a way where we can plot and order based on integrated data and look at expression using data slots from either the RNA or SCT assay..... |
Did anyone find the link to tutorial to convert seurat v3 object to monocle 2? |
@parveendabas try this:
|
Hello, I have been using this script and I am stuck at one place. This throws an error: Error in cds_from_seurat@reducedDims@listData[["UMAP"]] <- seurat@reductions[["umap"]]@cell.embeddings : Is there anything I am missing here? Thank you for your help. |
Hi, I was recently informed that they have rewritten the package and some of the objects might have changed. I encourage you to take a look at the construct of the object and can maybe change the objects you input in accordingly. Hope this helps! |
Thank you for getting back at me this quick. reduceDims = reduce_dim_aux but still not going through and giving me the same error. I am trying to figure out a way but it would be great if you could check it once and let me know. Thanks |
Reinstall monocle3 by doing this: Worked for me,correcting the no slot of name "reducedDims" for this object of class "cell_data_set" error Don't forget to relaunch R and reload monocle3 |
Try this instead: I was getting the same error as you but this worked for me. |
Hi everyone, pd <- data.frame(seurat.object@meta.data) #Construct monocle cds ` |
I had same problem. No luck with force reinstall as ondina-draia or monocle3 issue #246 suggested. I tried a revision similar to @akshatkarambe 's:
|
Would someone please provide a template on the format of Update: I solved this after reading official doc: My code:
|
Hi, Error in cds_from_seurat@reducedDims@listData[["UMAP"]] <- seurat@reductions[["umap"]]@cell.embeddings : any idea? |
@rwo012 I was using Harmony for integrating multiple samples and then i wanted to run Monocle on these integrated samples
Here I already have the UMAP i want along with the louvain clusters and I wish to use these with Monocle. I see that I have just one assay "RNA" . How do I use this particular clustering information instead of remaking clusters? The error msg I get is given below:
|
I temporarily use this solution for better intercompatibility library(DropletUtils) plant_cds <- load_cellranger_data('C:/Users/rahul/plant/') |
Hi all, I stopped trying to use monocle because it's too much of a pain to try and manually recreate a cds with appropriate data, so I'm using dynverse which honestly makes things 300% easier. Still, it needs the batch-corrected data because otherwise the trajectory looks a bit non-sensical. |
@seigfried Do you have an update on your harmony integrated object using in Monocle3? Any success? |
Has anyone performed pseudotemporal ordering analysis with Monocle 3 using an object made from Seurat 3's integration function?
I'm wondering if designating only 2000 features for the integration parameter will become problematic for doing downstream analyses with Monocle 3. Thanks in advance for your help.
The text was updated successfully, but these errors were encountered: