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kevinblighe / scDataviz

scDataviz: single cell dataviz and downstream analyses
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error messaege on: contourPlot #14

Closed fzhang988 closed 3 years ago

fzhang988 commented 3 years ago

When I was running this code following your instruction, got the error message:

ggout1 <- contourPlot(sce, reducedDim = 'UMAP', bins = 150, subtitle = 'UMAP performed on expression values', legendLabSize = 18, axisLabSize = 22, titleLabSize = 22, subtitleLabSize = 18, captionLabSize = 18)

--input data class is SingleCellExperiment

Error in value[3L] :

invalid subscript 'type' in 'reducedDim(, type="character", ...)':

'UMAP' not in 'reducedDimNames()'

image

fzhang988 commented 3 years ago

I found out the reason: I forgot to run this command: sce <- performUMAP(sce)

After I running the above command. it ran well.

Thanks, Fan