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Error when using harmony integrated Seurat object #68

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jmzvillarreal opened this issue May 4, 2023 · 0 comments
Open

Error when using harmony integrated Seurat object #68

jmzvillarreal opened this issue May 4, 2023 · 0 comments

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@jmzvillarreal
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Hi,
First of all, thanks a lot for shinycell ! It has made my life a lot easier in terms of sharing my sc analyses...
I am trying to buid an app for a seurat objet that has been integrated using harmony and it seems to fail loading the umap reduction coordinetes properly:
Screenshot from 2023-05-04 09-30-02
I have tried the following:

Projection <- as.data.frame(seu@reductions$[email protected])
UMAP_1 <- as.data.frame(Projection$UMAP_1)
rownames(UMAP_1) <- colnames(seu)
UMAP_2 <- as.data.frame(Projection$UMAP_2)
rownames(UMAP_2) <- colnames(seu)

makeShinyFiles(seu, scConf1, gex.assay = "RNA", gex.slot = "data",
gene.mapping = TRUE, shiny.prefix = "sc1",
shiny.dir = "shinyAppMulti/",
default.gene1 = "Acta2", default.gene2 = "Upk3a",
default.multigene = c("Vim","Krt5","Tnnt2","Acta1","Rgs5","Tesc"),
default.dimred = c("UMAP_1", "UMAP_2"))

But it still gives the same error...
Thanks a lot in advance !
Best,
Jaime.

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