Spatial QC pipeline — run_spatial_qc

This function implements all the analysis steps for perfoming QC. These include: 1. reading all sample information from metadata object/file and generating one Seurat object per sample. 2. Performs SoupX (ambient RNA removal) and Scrublet (doublet detection) if user defines the corresponding parameters. 3. Filter Seurat object according to QC criteria 4. Generate correspond QC plots.

Usage

run_spatial_qc_pipeline(
  data_dir,
  sample_meta,
  sample_meta_filename = NULL,
  nfeat_thresh = 500,
  mito_thresh = 5,
  meta_colnames = c("donor", "condition", "pass_qc"),
  out_dir = NULL,
  qc_to_plot = c("nFeature_Spatial", "nCount_Spatial", "percent.mito"),
  alpha = c(0.1, 0.9),
  pt.size.factor = 1.1,
  max.cutoff = "q98",
  min.cutoff = NA,
  spatial_col_pal = "inferno",
  crop = FALSE,
  tenx_dir = "outs",
  obj_filename = "seu_qc",
  ...
)

Arguments

data_dir: Parent directory where all sample 10x files are stored. Think of it as project directory.
sample_meta: Sample metadata information in a Data.frame like object. Columns should at least contain 'sample', 'donor', 'condition' and 'pass_qc'.
sample_meta_filename: Filename of sample metadata information, same as 'meta' parameter above. User should provide one of 'meta' or 'meta_filename'.
nfeat_thresh: Filter cells that have less than 'nfeat_thresh' counts expressed.
mito_thresh: Filter cells with more than 'mito_thresh'% counts.
meta_colnames: Sample metadata column names to store in Seurat metadata.
out_dir: Output directory for storing analysis results.
qc_to_plot: Vector of features in metadata to plot.
alpha: Controls opacity of spots. Provide as a vector specifying the min and max range of values (between 0 and 1).
pt.size.factor: Scale the size of the spots.
max.cutoff: Vector of maximum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').
min.cutoff: Vector of minimum cutoff values for each feature, may specify quantile in the form of 'q##' where '##' is the quantile (eg, 'q1', 'q10').
spatial_col_pal: (Spatial) Continuous colour palette to use from viridis package to colour spots on tissue, default "inferno".
crop: (Spatial) Crop the plot in to focus on points plotted. Set to FALSE to show entire background image.
tenx_dir: Name of 10x base directory, e.g. with outputs after running cellranger. Default 'premrna_outs', i.e. assumes single-nuclei RNA-seq.
obj_filename: Filename of the stored Seurat object, default 'seu_qc'.
...: Additional named parameters passed to Seurat, Scrublet or SoupX.

Value

List of Seurat objects as the length of the number of samples in the sample metadata file. If a single sample, return a Seurat object instead of a list.

Author

C.A.Kapourani C.A.Kapourani@ed.ac.uk