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Questions - seurat

Forcing ggplot to display graphs with no data?

I am working on displaying some UMAPs from Seurat object HVvU01temp using the following: Idents(HVvU01temp) <- HVvU01temp@meta.data$integrated_snn_res.0.9 temptemp <- HVvU01temp[,HVvU01temp@meta...
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Annaliese

r

ggplot2

seurat

Votes: 0

Answers: 0

scv.pl.proportions(): numpy.AxisError in `Cellrank` workflow

I am new to use python to anlyze scRNA-seq. I run the cellrank workflow and always found this error. Here is my code for Cellrank: import scvelo as scv import scanpy as sc import cellrank import nump...
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jpx

seurat

scanpy

Votes: 0

Answers: 1

Latest Answer

scv.pl.proportions gives the proportion of spliced and unspliced reads in your dataset. These count tables must be added to your adata layers before you can call this function. Your adata object does ...
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badwolf

Conditional subsetting of Seurat object

I have a Seurat object that I have run through doubletFinder. I am trying to subset the object based on cells being classified as a 'Singlet' under seurat_object@meta.data[["DF.classifications_0...
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cer

r

subset

seurat

Votes: 0

Answers: 2

Latest Answer

This worked. seurat_object = seurat_object[, seurat_object@meta.data[, meta_data] == "Singlet"] But I especially don't get why this one did not work: seurat_object <- subset(seurat_objec...
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cer

ggplot2 overlapping causing issues with ridgeplot

I am creating ridge plots from the Seurat package. This packages utilizes ggplot2. All of my ridge plots look great except for one. I am trying to manually adjust the bandwidth to make this plot look ...
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Allen Schweickart

r

ggplot2

seurat

Votes: 0

Answers: 1

Latest Answer

I indirectly solved the issue I was having by changing the size of the bandwidth and the colors of the plots. I made some colors translucent so that you can see the peaks behind them. Example: This c...
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Allen Schweickart

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