scTrimClust: scTrimClust: Cluster visualization with alpha hull-based...

In RepeatedHighDim: Methods for High-Dimensional Repeated Measures Data

scTrimClust: Cluster visualization with alpha hull-based outlier detection

Description

Visualizes cell clusters in low-dimensional space (t-SNE, UMAP, etc.) and identifies/removes potential outliers based on their distance from cluster alpha hulls.

Usage

scTrimClust(
  object,
  dims = c(1, 2),
  cells = NULL,
  cols = NULL,
  pt.size = NULL,
  reduction = NULL,
  group.by = NULL,
  split.by = NULL,
  shape.by = NULL,
  order = NULL,
  shuffle = FALSE,
  seed = 1,
  label = FALSE,
  label.size = 4,
  label.color = "black",
  label.box = FALSE,
  repel = FALSE,
  alpha = 1,
  stroke.size = NULL,
  cells.highlight = NULL,
  cols.highlight = "#DE2D26",
  sizes.highlight = 1,
  na.value = "grey50",
  ncol = NULL,
  combine = TRUE,
  raster = NULL,
  raster.dpi = c(512, 512),
  add.alpha.hull = TRUE,
  hull.alpha = 2,
  hull.color = NULL,
  hull.size = 0.5,
  outlier.quantile = 0.4,
  remove.outliers = FALSE,
  outlier.alpha = 0.1,
  outlier.color = NULL,
  outlier.colors = NULL,
  outline.color = NULL,
  outline.size = 0.5,
  outline.alpha = 1,
  outline.outliers = FALSE
)

Arguments

object	A Seurat object containing dimensionality reduction results.
dims	Integer vector of length 2 specifying which dimensions to plot (e.g., c(1, 2)).
cells	Vector of cells to include (NULL uses all cells).
cols	Vector of colors for clusters.
pt.size	Point size for cells.
reduction	Name of dimensionality reduction to use (e.g., "umap", "tsne").
group.by	Metadata column to group cells by (default: 'ident' uses cluster IDs).
split.by	Metadata column to split plots by (creates multiple facets).
shape.by	Metadata column to determine point shapes.
order	Vector specifying order to plot cells (affects z-ordering).
shuffle	Logical to randomly shuffle plotting order.
seed	Random seed for reproducibility when shuffle=TRUE.
label	Logical to add cluster labels.
label.size	Size of cluster labels.
label.color	Color of cluster labels.
label.box	Logical to add background box to labels.
repel	Logical to use ggrepel for label placement.
alpha	Transparency level for points (0-1).
stroke.size	Size of point borders.
cells.highlight	Specific cells to highlight.
cols.highlight	Color(s) for highlighted cells.
sizes.highlight	Size(s) for highlighted cells.
na.value	Color for NA values.
ncol	Number of columns for faceted plots.
combine	Logical to combine multiple plots into one.
raster	Logical to rasterize points (for large datasets).
raster.dpi	Resolution for rasterized points.
add.alpha.hull	Logical to compute and plot alpha hulls.
hull.alpha	Alpha parameter for hull calculation. Higher values produce smoother hulls that encompass more cells (default: 2).
hull.color	Color of the alpha hull lines (default: Null = same color as cluster points).
hull.size	Thickness of the alpha hull lines (default: 0.5).
outlier.quantile	Quantile threshold (0-1) for outlier detection based on hull distance. Cells with distances below this quantile are considered outliers (default: 0.4).
remove.outliers	Logical - whether to remove outliers from the returned Seurat object (default: FALSE).
outlier.alpha	Transparency level for outlier points (0-1; default: 0.1).
outlier.color	Single color to use for all outlier points. If NULL, uses cluster colors.
outlier.colors	A named vector of colors to be assigned to outliers.If NULL, uses cluster colors.
outline.color	Color for the outline of points. If NULL, no outline is added.
outline.size	Thickness of the outline around points (default: 0.5).
outline.alpha	Transparency of the outline around points (default: 1).
outline.outliers	Logical whether to add outlines to outlier points (default: FALSE).

Value

A list containing:

• plot: ggplot object of the visualization with hulls and highlighted outliers

• object: Modified Seurat object with outliers removed (if remove.outliers=TRUE)

• outlier_coords: Dataframe containing coordinates of outlier cells, their IDs and cluster assignments

• hull_info: List containing alpha hull geometries (if add.alpha.hull=TRUE)

Examples

## Not run: 

scTrimClust(RepeatedHighDim:::seurat_obj,reduction = 'tsne',
group.by = 'CellType',
hull.alpha = 2,
remove.outliers = FALSE,
outlier.quantile = 0.2,
outlier.alpha = 0.3,
outlier.color = "red",
pt.size = 5,
outline.color = "black",
outline.outliers = TRUE)

# second example with custom outlier col per cluster

scTrimClust(RepeatedHighDim:::seurat_obj,reduction = 'tsne',
group.by = 'CellType',
hull.alpha = 2,
remove.outliers = FALSE,
outlier.quantile = 0.2,
outlier.alpha = 0.3,
outlier.colors = c('TypeA'="black",
'TypeB'='violet','TypeC' ='pink'),
pt.size = 5,
outline.color = "black",
outline.outliers = TRUE)$plot


## End(Not run)

RepeatedHighDim documentation built on April 15, 2025, 1:28 a.m.