enrichment spatial plots and UMAPs for Visium data in Seurat?

[krigia]

Hello @troels @pmarks @mxposed @zeehio @smoe

Does Seurat have any option/function to generate enrichment spatial plots and UMAPs for Visium data? Similar to those generated by another pipeline for spatial analysis:

Thank you.

[pmarks]

@krigia what feature are you using to color the spots in this case? Generally any quantity you can calculate on a per-spot basis can be used as a color variable for either UMAP or spatial plots. There are lot's of examples on the vignette, but I'm not sure if that specifically covers what you're looking to do.

[krigia]

@pmarks @troels I use a list of ~350 genes to color the spots and estimate a gene signature. The plots above were generated using certain Giotto functions, but now I am using Seurat extensively and I want to reproduce the same results. I checked the examples on the vignette but none can estimate a gene signature. Any advice how to modify an existing function to estimate the average expression of multiple genes across spots? Thank you.

[AustinHartman]

Hi @krigia I'd recommend you check out the AddModuleScore function to compute a single score for a collection of genes for each spot

[krigia]

@AustinHartman Thank you! This is helpful. However I am getting an error when I run cd_features <- list(c( 'FN1', 'VIM', 'PRRX1', 'SNAI2')) se_F1_normalizedmodule <- AddModuleScore( object = se_F1_normalized, features = cd_features, rownames(x=se_F1_normalized), ctrl = 100, name = 'ADRN_Features' ) head(x = se_F1_normalizedmodule[])

}

png("F1_UMAP-spatialpot-MES_plot.png", width=9, height=9, units="in", res=300) p3 <- ST.FeaturePlot(se_F1_normalizedmodule, features = cd_features, ncol = 2, grid.ncol = 2, show.sb = TRUE) p1 <- FeaturePlot(se_F1_normalizedmodule, features = "cd_features", cols = c("mistyrose", "red", "darkred")) p2 <- VlnPlot(se_F1_normalizedmodule, features = "cd_features", ncol = 2, group.by = "seurat_clusters") (p1 - p2)/p3 dev.off()

Error in vars.alt[[var]] : no such index at level 1

I would greatly appreciate your feedback. Thank you again!

[krigia]

Thank you! However I am getting an error when I run cd_features <- list(c( 'FN1', 'VIM', 'PRRX1', 'SNAI2')) se_F1_normalizedmodule <- AddModuleScore( object = se_F1_normalized, features = cd_features, rownames(x=se_F1_normalized), ctrl = 100, name = 'ADRN_Features' ) head(x = se_F1_normalizedmodule[])

}

png("F1_UMAP-spatialpot-MES_plot.png", width=9, height=9, units="in", res=300) p3 <- ST.FeaturePlot(se_F1_normalizedmodule, features = cd_features, ncol = 2, grid.ncol = 2, show.sbhttp://show.sb/ = TRUE) p1 <- FeaturePlot(se_F1_normalizedmodule, features = "cd_features", cols = c("mistyrose", "red", "darkred")) p2 <- VlnPlot(se_F1_normalizedmodule, features = "cd_features", ncol = 2, group.byhttp://group.by/ = "seurat_clusters") (p1 - p2)/p3 dev.off() Error in vars.alt[[var]] : no such index at level 1 I would greatly appreciate your feedback. Thank you again!

From: Austin Hartman @.> Reply-To: satijalab/seurat @.> Date: Friday, June 23, 2023 at 12:27 PM To: satijalab/seurat @.> Cc: "Giannikou, Krinio" @.>, Mention @.***> Subject: Re: [satijalab/seurat] enrichment spatial plots and UMAPs for Visium data in Seurat? (Issue #7463)

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Hi @krigiahttps://secure-web.cisco.com/1hVQNuV-RCurNYItBIRN1dT7IjXu6vFKYckvnhi71H76Hz7yer_m1PuYXSyxgF54DIYosWQ0ZJ0DRb1EhX5_fk4wwnoe-KLwtHPkEC6_w6w68nLV9Vdwxix0_dT7qMIbDdydQ4ud3pjQDBll27tp0b7J14c7cBBRwVgcJm8jNqmpzv9bklbxm4PjDu9MieUmOwIvLBYNldKEhXIUYO5WDW3DygZT_E_DL_CNW1NidZqu75OAJVAvpJXb8oODnOwav-xMX-LX5FD6lg-M0m5NTRLC_hgFx2rF-rAxD_pmQTNsP9QO93Y2ea31SgY3sHubQ70gdcqzV-Kgi7WrJUfc_3g/https%3A%2F%2Fgithub.com%2Fkrigia I'd recommend you check out the AddModuleScorehttps://secure-web.cisco.com/1TeXvvTRKeSw-0nmSCbQk0gH3H6ynfJNWCj6PoYTCBxX5hLMTSo6_GraIhXX545rTaO_Bp6BfFviorcKaIkCFliF6pDJ59GLfTEsewGPVsBPSxo_mgkd2qkSdezqZsTWAIK-js6AcVVdomCSisZSLw0GQNdo2JtFNdeTSJ77l2vv8rvyBFnNlddFCgL8uVG8T5hiyBdexf4smzMwgfqYiAtRf2voWxyjXZUxnl_HHkDMXXDH7I75yxav-mOhqIoCm66EFzDptvx1kYpxLXfZB9Ax_yMQAxdxIIK1Q3o9j0XIuARHqXB5KbB_SRK5bICV6_Bbw_-gYu9mtauapdkGGtA/https%3A%2F%2Fsatijalab.org%2Fseurat%2Freference%2Faddmodulescore function to compute a single score for a collection of genes for each spot

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[NyKepler]

Unlist your feature list and it should work.