How to get location information and mouse ligand receptor pair information?

[maqingyue]

Hi, I'm trying to use my own spatial transcriptome data for SpaGene analysis. How do I get the location information? I don't know whether the imageow, imagecol and gene extracted in the seurat data format correspond to each other, or can you tell me how to extract them?

In addition, you use human ligand receptor pair data in the tutorial. Is there any mouse ligand receptor pair data that can be shared? Or is it the same library for humans and mice? I don't know much about it.

I'm looking forward to your reply, thanks!

[maqingyue]

To add, my data is the integrated data of six samples, and the tutorial is a sample. I don't know if it has any impact.

[liuqivandy]

Imagerow and imagecol is the location. You can use any ligand-receptor pair. There are many databases available. What I used is celltalkdb. http://tcm.zju.edu.cn/celltalkdb/ Best, Qi

From: maqingyue @.> Date: Wednesday, February 22, 2023 at 2:25 AM To: liuqivandy/SpaGene @.> Cc: Subscribed @.***> Subject: [liuqivandy/SpaGene] How to get location information and mouse ligand receptor pair information? (Issue #5)

Hi, I'm trying to use my own spatial transcriptome data for SpaGene analysis. How do I get the location information? I don't know whether the imageow, imagecol and gene extracted in the seurat data format correspond to each other, or can you tell me how to extract them?

In addition, you use human ligand receptor pair data in the tutorial. Is there any mouse ligand receptor pair data that can be shared? Or is it the same library for humans and mice? I don't know much about it.

I'm looking forward to your reply, thanks!

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[maqingyue]

I wrote a piece of code to extract localiaon. Is the extraction method correct?

dimname <- sample@assays[["Spatial"]]@data@Dimnames[[2]] imagecol <- seurat_obj@meta.data[["imagecol"]] imagerow <- seurat_obj@meta.data[["imagerow"]] location <- data.frame(dimname, imagecol, imagerow) rownames(location) <- location[,1] location <- location[,-1]

My data is the integrated data of six samples, and the tutorial is a sample. I don't know if it has any impact. The pattern information I get is shown in the figure below. Each pattern is the superposition of six sample images. What I want is to display the pattern on each sample image.

[liuqivandy]

Seurat has the function to extract the location GetTissueCoordinates

From: maqingyue @.> Date: Wednesday, February 22, 2023 at 7:09 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] How to get location information and mouse ligand receptor pair information? (Issue #5)

I wrote a piece of code to extract localiaon. Is the extraction method correct?

dimname <- @.**@*.**@*.[[2]] imagecol <- @*.**@*.>[["imagecol"]] imagerow <- @*.**@*.***>[["imagerow"]] location <- data.frame(dimname, imagecol, imagerow) rownames(location) <- location[,1] location <- location[,-1]

My data is the integrated data of six samples, and the tutorial is a sample. I don't know if it has any impact. The pattern information I get is shown in the figure below. Each pattern is the superposition of six sample images. What I want is to display the pattern on each sample image.

[fig]https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F113956599%2F220799651-0e63eb35-1f0e-43ae-b482-97a2456e6140.png&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7Ccb44bee2b0fe497b468d08db153aa3d0%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C638127113844475362%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LdhwzpNrw%2FvzXTvJFor7Xgtkub75g84WVQ88YCIYSEU%3D&reserved=0

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[maqingyue]

Thank you very much. I have got the data of mouse ligand receptor pairs and know how to extract the location. But when doing SpaGene with the counts matrix I extracted, the error is reported as follows:

Error in SpaGene(counts, location) : the ncol of expr should match the nrow of location

My code is as follows:

location <- GetTissueCoordinates(seurat_obj) counts <- GetAssayData(object = seurat_obj, slot = "counts") bc_spagene<-SpaGene(counts,location)

[liuqivandy]

Please check dim(counts) and dim(location), the ncol of counts should match the nrow of location

From: maqingyue @.> Date: Wednesday, February 22, 2023 at 8:13 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] How to get location information and mouse ligand receptor pair information? (Issue #5)

Thank you very much. I have got the data of mouse ligand receptor pairs and know how to extract the location. But when doing SpaGene with the counts matrix I extracted, the error is reported as follows:

Error in SpaGene(counts, location) : the ncol of expr should match the nrow of location

My code is as follows:

location <- GetTissueCoordinates(seurat_obj) counts <- GetAssayData(object = seurat_obj, slot = "counts") bc_spagene<-SpaGene(counts,location)

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[maqingyue]

It doesn't seem to match, but I can't find the reason.

dim(counts) [1] 16516 6762 dim(location) [1] 961 2

[liuqivandy]

This is only for one spatial transcriptomics data. If you have multiple spatial omics data, please follow the tutorial how to deal with multiple spatial omics data.

From: maqingyue @.> Date: Wednesday, February 22, 2023 at 8:20 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] How to get location information and mouse ligand receptor pair information? (Issue #5)

It doesn't seem to match, but I can't find the reason.

dim(counts) [1] 16516 6762 dim(location) [1] 961 2

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[maqingyue]

Ok, I have found your multi-sample tutorial. Thank you very much for your patience. Have a good day.

Sincerely, Qingyue Ma

[maqingyue]

Hi, there is no recognition of co-located ligand-receptor pairs in the multi-sample tutorial (https://htmlpreview.github.io/?https://github.com/liuqivandy/SpaGene/blob/master/Tutorial/mb_anterior_posterior.html). I tried to use this code, but it didn't work. Can you give me some suggestions?

countlist<-list(count1,count2,count3) locationlist<-list(location1[,2:1],location2[,2:1],location3[,2:1]) bc_lr<-SpaGene_LR(countlist,locationlist,LRpair=LRpair)

[liuqivandy]

Please follow the tutorials on multiple samples. You cannot combine location unless the location from one sample to another has some meaning.

From: maqingyue @.> Date: Wednesday, February 22, 2023 at 10:56 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] How to get location information and mouse ligand receptor pair information? (Issue #5)

Hi, there is no recognition of co-located ligand-receptor pairs in the multi-sample tutorial (https://htmlpreview.github.io/?https://github.com/liuqivandy/SpaGene/blob/master/Tutorial/mb_anterior_posterior.htmlhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fhtmlpreview.github.io%2F%3Fhttps%3A%2F%2Fgithub.com%2Fliuqivandy%2FSpaGene%2Fblob%2Fmaster%2FTutorial%2Fmb_anterior_posterior.html&data=05%7C01%7Cqi.liu%40vanderbilt.edu%7C0eed2726eaed4baea26f08db155a56d7%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C638127249975266923%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Fo47sGAP8YZPS4LyuZfTKRFrHvw3HVVgD72%2FJlj8oIU%3D&reserved=0). I tried to use this code, but it didn't work. Can you give me some suggestions?

countlist<-list(count1,count2,count3) locationlist<-list(location1[,2:1],location2[,2:1],location3[,2:1]) bc_lr<-SpaGene_LR(countlist,locationlist,LRpair=LRpair)

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[maqingyue]

My three samples belong to biological duplication. I don't know if they are consistent with what you said. Can this location be merged? If it can be combined, how to find the subsequent ligand receptor pairs? This is not mentioned in the multi-sample tutorial. If it cannot be combined, does it need to analyze each sample separately when looking for ligand receptor pairs?

[liuqivandy]

I think it cannot be combined. You can analyze each sample separately.

From: maqingyue @.> Date: Thursday, February 23, 2023 at 6:53 PM To: liuqivandy/SpaGene @.> Cc: Liu, Qi (University) @.>, Comment @.> Subject: Re: [liuqivandy/SpaGene] How to get location information and mouse ligand receptor pair information? (Issue #5)

My three samples belong to biological duplication. I don't know if they are consistent with what you said. Can this location be merged? If it can be combined, how to find the subsequent ligand receptor pairs? This is not mentioned in the multi-sample tutorial. If it cannot be combined, does it need to analyze each sample separately when looking for ligand receptor pairs?

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[maqingyue]

Ok, thanks for your patience.