Plot Outlier Metrics to PDF

This function generates a PDF file containing plots for each sample in the SpatialExperiment object, highlighting outliers based on specified metrics. Each plot visualizes outlier metrics for a single sample, allowing for easy comparison and analysis across samples.

Usage

plotQCpdf(
  spe,
  sample_id = "sample_id",
  metric = "detected",
  outliers = "local_outliers",
  colors = c("white", "black"),
  stroke = 1,
  point_size = 2,
  width = 5,
  height = 5,
  fname
)

Arguments

spe

A SpatialExperiment object containing the data to be plotted.

sample_id

A character string specifying the column name in colData(spe) that contains unique sample identifiers. Default is 'sample_id'.

metric

A character string specifying the metric to be visualized in the plot. This metric should be a column name in colData(spe).

outliers

A character string specifying the column name in colData(spe) that indicates whether a data point is considered an outlier. Default is local_outliers'.

colors

A character vector specifying the colors to be used for the gradient scale. If length is 2, the gradient will be a single color gradient

stroke

A numeric value specifying the border thickness for outlier points. Default is 1.

point_size

A numeric value specifying the size of the points in the plot. Default is 2.

width

A numeric value indicating the width of the plot. Default is 5.

height

A numeric value indicating the height of the plot. Default is 5.

fname

A character string specifying the path and name of the output PDF file.

Value

ggplot object if specified. Generates a plot otherwise.

Examples

library(SpotSweeper)
library(SpatialExperiment)
library(escheR)

# load example data
spe <- STexampleData::Visium_humanDLPFC()
#> see ?STexampleData and browseVignettes('STexampleData') for documentation
#> loading from cache

tempFilePath <- file.path(tempdir(), "examplePlot.pdf")

# change from gene id to gene names
rownames(spe) <- rowData(spe)$gene_name

# drop out-of-tissue spots
spe <- spe[, spe$in_tissue == 1]
spe <- spe[, !is.na(spe$ground_truth)]

# Identifying the mitochondrial transcripts in our SpatialExperiment.
is.mito <- rownames(spe)[grepl("^MT-", rownames(spe))]

# Calculating QC metrics for each spot using scuttle
spe <- scuttle::addPerCellQCMetrics(spe, subsets = list(Mito = is.mito))
colnames(colData(spe))
#>  [1] "barcode_id"            "sample_id"             "in_tissue"            
#>  [4] "array_row"             "array_col"             "ground_truth"         
#>  [7] "reference"             "cell_count"            "sum"                  
#> [10] "detected"              "subsets_Mito_sum"      "subsets_Mito_detected"
#> [13] "subsets_Mito_percent"  "total"                

# Identifying local outliers using SpotSweeper
spe <- localOutliers(spe,
                     metric = "sum",
                     direction = "lower",
                     log = TRUE
)

plotQCpdf(spe,
          metric="sum",
          outliers="sum_outliers",
          fname=tempFilePath)
#> Warning: 'plotQC' is deprecated.
#> Use 'plotQCmetrics' instead.
#> See help("Deprecated")
#> pdf 
#>   2