Visualize metacell partitions on a dimensionality reduction

Usage

MetaCellPlot(
  srt,
  reduction = NULL,
  show_cells = FALSE,
  group.by = NULL,
  color.by = NULL,
  dims = c(1, 2),
  label = FALSE,
  palette = "Chinese",
  palcolor = NULL,
  palette_metacell = "Chinese",
  palcolor_metacell = NULL,
  pt.size = 1.2,
  pt.alpha = 1,
  cell.alpha = 1,
  cell.size = 0.7,
  stroke = 0.5,
  show_metacell_size = TRUE,
  metacell_size_range = NULL,
  cell_param = list(),
  metacell_param = list(),
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  return_layer = FALSE,
  ...
)

Arguments

srt: A Seurat object with metacell results from RunMetaCell().
reduction: Which dimensionality reduction to use. If not specified, will use the reduction returned by DefaultReduction.
show_cells: Logical. If TRUE, the original single-cell points are drawn as a semi-transparent background layer behind the metacell centroids.
group.by: Name of one or more meta.data columns to group (color) cells by.
color.by: Metadata column in the metacell Seurat used to color centroids. If NULL, metacell centroids use one fixed color.
dims: Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
label: Whether to label the cell groups.
palette: Color palette name. Available palettes can be found in thisplot::show_palettes. Default is "Chinese".
palcolor: Custom colors used to create a color palette. Default is NULL.
palette_metacell: Color palette for the metacell centroid layer. Default is "Chinese".
palcolor_metacell: Custom colors for the metacell centroid layer.
pt.size: The size of the points in the plot.
pt.alpha: The transparency of the data points. Default is 1.
cell.alpha: Alpha value for the original single-cell background layer.
cell.size: Point size for the original single-cell background layer.
stroke: Point border stroke width for metacell centroids.
show_metacell_size: Whether to map metacell_size to centroid size.
metacell_size_range: Point-size range used when show_metacell_size = TRUE.
cell_param: A named list of extra arguments passed to CellDimPlot() for the original single-cell background layer.
metacell_param: A named list of extra arguments passed to CellDimPlot() for the metacell centroid/query layer.
legend.position: The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".
legend.direction: The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
return_layer: Logical. If TRUE, returns a named list of ggplot2 layers/scales (cells, fill_scale, centroids, scale_fill, scale_size, labels) instead of a complete plot.
...: Additional arguments passed to ggplot2::geom_point() for metacell centroids.

Value

A ggplot object, or a named list of ggplot2 layers when return_layer = TRUE.

Examples

data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub, verbose = FALSE)
mc <- RunMetaCell(
  pancreas_sub,
  method = "supercell",
  gamma = 20
)

MetaCellPlot(
  mc,
  group.by = "CellType",
  palette_metacell = "ChineseSet8"
)

MetaCellPlot(
  mc,
  group.by = "CellType",
  reduction = "umap",
  palette = "ChineseSet8",
  show_cells = TRUE
)

CellDimPlot(
  pancreas_sub, group.by = "CellType"
) +
  MetaCellPlot(
    mc,
    group.by = "CellType",
    return_layer = TRUE,
    palette_metacell = "ChineseSet8"
  )