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Plot UMIs per UPIa for quality control

TauPlot.Rd

Plot UMIs per UPIa for quality control

Usage

TauPlot(object, ...)

# S3 method for class 'data.frame'
TauPlot(object, group_by = NULL, ...)

# S3 method for class 'Seurat'
TauPlot(object, group_by = NULL, ...)

Arguments

object

A data.frame-like object or a Seurat object with umi_per_upia, tau and tau_type values

...

Not yet implemented

group_by

A column in the object representing a 'character' or 'factor' to group data by

Value

A ggplot object

See also

Other QC-plots: CellCountPlot()

Examples


library(pixelatorR)

# Load example data as a Seurat object
pxl_file <- system.file("extdata/five_cells",
  "five_cells.pxl",
  package = "pixelatorR"
)
seur_obj <- ReadMPX_Seurat(pxl_file)
#> ✔ Created a 'Seurat' object with 5 cells and 80 targeted surface proteins
seur_obj
#> An object of class Seurat 
#> 80 features across 5 samples within 1 assay 
#> Active assay: mpxCells (80 features, 80 variable features)
#>  2 layers present: counts, data

# Plot with data.frame
TauPlot(seur_obj[[]])


# Plot with Seurat object
TauPlot(seur_obj)


# Group by sample in merged data
seur_obj1 <- seur_obj2 <- seur_obj
seur_obj1$sample <- "1"
seur_obj2$sample <- "2"
seur_obj_merged <- merge(seur_obj1, seur_obj2, add.cell.ids = c("A", "B"))
TauPlot(seur_obj_merged, group_by = "sample")