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added seurat import in data handler #113

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added seurat import in data handler #113

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252872b
added seurat import in data handler
Mar 3, 2022
45b1521
moved to Seurat:: for imports
Mar 5, 2022
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8 changes: 4 additions & 4 deletions R/methods-Vision.R
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Original file line number Diff line number Diff line change
Expand Up @@ -595,7 +595,7 @@ setMethod("Vision", signature(data = "Seurat"),
stop("Package \"Seurat\" needed to load this data object. Please install it.",
call. = FALSE)
}

obj <- data
args <- list(...)

Expand All @@ -621,13 +621,13 @@ setMethod("Vision", signature(data = "Seurat"),
}

# Get latent space
if (is.null(dimRed) && "pca" %in% Reductions(obj)) {
if (is.null(dimRed) && "pca" %in% Seurat:Reductions(obj)) {
dimRed <- "pca"
}

if (!("latentSpace" %in% names(args))){

latentSpace <- Embeddings(obj,
latentSpace <- Seurat::Embeddings(obj,
reduction = dimRed
)

Expand All @@ -653,7 +653,7 @@ setMethod("Vision", signature(data = "Seurat"),

message(sprintf("Adding Visualization: %s", name))

coordinates <- Embeddings(obj,
coordinates <- Seurat:Embeddings(obj,
reduction = method)

vis <- addProjection(vis,
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