slingshot plot(reducedDim(sds) error #6
Description
I am interested to run slingshot trajectory using your guideline using my Seurat object (Normalized, PCA, tSNE, UMAP, clustering done)
https://bustools.github.io/BUS_notebooks_R/slingshot.html
seu
An object of class Seurat
23572 features across 13696 samples within 1 assay
Active assay: RNA (23572 features, 1257 variable features)
3 dimensional reductions calculated: pca, tsne, umap
names(seu@meta.data)
[1] "orig.ident" "nCount_RNA"
[3] "nFeature_RNA" "sample"
[5] "tech" "tomato"
[7] "percent.mito" "percent.ribo"
[9] "pANN_0.25_0.24_3170" "DF.classifications_0.25_0.24_3170"
[11] "RNA_snn_res.0.5" "seurat_clusters"
[13] "silhouette_score" "RNA_snn_res.0.4"
[15] "scina_labels"
sds <- slingshot(Embeddings(seu, "umap"), clusterLabels = seu$seurat_clusters,
start.clus = 3, stretch = 0)
cell_pal <- function(cell_vars, pal_fun,...) {
if (is.numeric(cell_vars)) {
pal <- pal_fun(100, ...)
return(pal[cut(cell_vars, breaks = 100)])
} else {
categories <- sort(unique(cell_vars))
pal <- setNames(pal_fun(length(categories), ...), categories)
return(pal[cell_vars])
}
}
cell_colors <- cell_pal(seu$scina_labels, brewer_pal("qual", "Set2"))
cell_colors_clust <- cell_pal(seu$seurat_clusters, hue_pal())
plot(reducedDim(sds), col = cell_colors, pch = 16, cex = 0.5)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'plot': unable to find an inherited method for function 'reducedDim' for signature '"PseudotimeOrdering", "missing"'
Could you help what I am missing. I have all the required library installed and called.
sessionInfo()
R version 4.2.2 (2022-10-31)
slingshot_2.6.0
BUSpaRse_1.12.2
SeuratObject_4.1.3
Seurat_4.3.0