Visualize Cell QC metrics of Seurat object

Usage

VizSeuratCellQC(
  object,
  features = c("nFeature_RNA", "nCount_RNA", "percent.mt", "percent.ribo", "percent.hb",
    "percent.plat"),
  plot_type = c("violin", "box", "scatter", "bar", "ridge", "table"),
  scatter_x = "nCount_RNA",
  palette = "Set1",
  ...
)

Arguments

object: A Seurat object with cell QC metrics
features: Features to visualize
plot_type: Type of plot to generate One of 'violin', 'box', 'scatter', 'bar', 'ridge' and 'table' If 'plot_type' is 'table', it will return a data frame with number of cells before and after filtering
scatter_x: Feature to use as x-axis in scatter plot. If it is one of the features, it will be removed from the features
palette: Color palette to use
...: Additional arguments to pass to the plot function

Value

The plot

Examples

# \donttest{
set.seed(8525)
sobj <- SeuratObject::pbmc_small
sobj$.QC <- sample(c(TRUE, FALSE), ncol(sobj), replace = TRUE)
sobj$Sample <- sample(c("Sample1", "Sample2"), ncol(sobj), replace = TRUE)
sobj$percent.mt <- runif(ncol(sobj), 0, 1)
sobj$percent.ribo <- runif(ncol(sobj), 0, 1)
sobj$percent.hb <- runif(ncol(sobj), 0, 1)
sobj$percent.plat <- runif(ncol(sobj), 0, 1)
sobj$nFeature_RNA <- as.integer(runif(ncol(sobj), 1000, 5000))
sobj$nCount_RNA <- as.integer(runif(ncol(sobj), 1000, 5000))

# Visualize cell QC metrics
VizSeuratCellQC(sobj)

VizSeuratCellQC(sobj, plot_type = "scatter")

VizSeuratCellQC(sobj, plot_type = "bar")

VizSeuratCellQC(sobj, plot_type = "ridge")
#> Picking joint bandwidth of 501
#> Picking joint bandwidth of 509
#> Picking joint bandwidth of 0.125
#> Picking joint bandwidth of 0.0973
#> Picking joint bandwidth of 0.12
#> Picking joint bandwidth of 0.128
#> Picking joint bandwidth of 501
#> Picking joint bandwidth of 509
#> Picking joint bandwidth of 0.125
#> Picking joint bandwidth of 0.0973
#> Picking joint bandwidth of 0.12
#> Picking joint bandwidth of 0.128

VizSeuratCellQC(sobj, features = c("percent.mt", "percent.ribo"))

VizSeuratCellQC(sobj, features = c("percent.mt", "percent.ribo"), plot_type = "box")

VizSeuratCellQC(sobj, plot_type = "table")
#> # A tibble: 3 × 4
#>   Sample      failed passed total
#>   <fct>        <int>  <int> <int>
#> 1 Sample1         14     26    40
#> 2 Sample2         21     19    40
#> 3 All_Samples     35     45    80

dim(sobj)
#> [1] 230  80
sobj <- FinishSeuratQC(sobj)
dim(sobj)
#> [1] 230  45
# }