How do I access inflection points in Seurat object?
0
0
Entering edit mode
2.4 years ago
gt ▴ 30

I ran the following code below to calculate inflection points for the UMI counts for my single cell data using Seurat.

seurat_obj <- CalculateBarcodeInflections(seurat_obj,barcode.column = "nCount_RNA",group.column = "orig.ident",threshold.low = NULL,threshold.high = NULL)

I want to obtain the inflection points so I can create my own ggplot. I know they provide a function to create a plot but I'd rather create my own for styling purposes. I tried the code below which is provided in the documentation.

seurat_obj@tools$CalculateBarcodeInflections$inflection_points

However, this only provides me a version of the metadata and a column for the ranking of the UMI. I want the actual inflection points. Does anyone know how to extract these from the Seurat object? Or do I have to manually identify them using the cells_pass item in the list? Seems kind of a pain.

Seurat scRNA-seq • 516 views
ADD COMMENT

Login before adding your answer.

Traffic: 2739 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6