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Batch spatial dimensionality-reduction (cell-type) plots

PlotSpatialDimPlots.Rd

Produces Seurat::SpatialDimPlot() panels for each image in the object, one figure per metadata variable in group_by_vars. Supports the same "auto" / "metadata" layout modes as PlotSpatialFeaturePlots(). When multiple variables are supplied, join_plots = TRUE tiles them into a single page.

Usage

PlotSpatialDimPlots(
  seurat_object,
  group_by_vars = NULL,
  layout_method = "auto",
  row.by = NULL,
  images_to_plot = NULL,
  remove_outliers = FALSE,
  outlier_prob = 0.01,
  size_override = NULL,
  uniform_size = FALSE,
  calcptsizesc = 100,
  colors = NULL,
  number_labels = FALSE,
  legendnrow = 3,
  legend.side = "bottom",
  legend.direction = "horizontal",
  join_plots = FALSE,
  join_nrow = NULL,
  join_ncol = NULL,
  output_dir = NULL,
  rowannsize = 16,
  imgalpha = 1,
  alpha = 1,
  object_name = "",
  group.by = NULL,
  cluster_colors = NULL,
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE
)

GenerateSpatialDimMaps(
  seurat_object,
  group_by_vars = NULL,
  layout_method = "auto",
  row.by = NULL,
  images_to_plot = NULL,
  remove_outliers = FALSE,
  outlier_prob = 0.01,
  size_override = NULL,
  uniform_size = FALSE,
  calcptsizesc = 100,
  colors = NULL,
  number_labels = FALSE,
  legendnrow = 3,
  legend.side = "bottom",
  legend.direction = "horizontal",
  join_plots = FALSE,
  join_nrow = NULL,
  join_ncol = NULL,
  output_dir = NULL,
  rowannsize = 16,
  imgalpha = 1,
  alpha = 1,
  object_name = "",
  group.by = NULL,
  cluster_colors = NULL,
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE
)

Arguments

seurat_object

A Seurat object with spatial images.

group_by_vars

Character vector. Metadata columns to plot.

layout_method

Character. "auto" or "metadata". Default "auto".

row.by

Character or NULL. Slide-level metadata column for row grouping (required for "metadata" layout).

images_to_plot

Character vector or NULL. Images to include.

remove_outliers

Logical. Trim outlier cells. Default FALSE.

outlier_prob

Numeric. Quantile trim level. Default 0.01.

size_override

Scalar or named numeric list. A plain number applies to all images; a named list applies per image.

uniform_size

Logical. Use the median point size across all images. Default FALSE.

calcptsizesc

Numeric. Scaling constant for automatic point-size calculation; larger values yield larger spots. Radius-aware, so the same value works across Visium and Visium HD. Default 100.

colors

Named character vector. Colors for each group level. NULL auto-resolves from PrepObject or Nour_pal. Supersedes the deprecated cluster_colors.

number_labels

Logical. Prefix each legend label with a zero-padded index (e.g., "01. CellType"). Default FALSE.

legendnrow

Integer or vector. Number of rows the categorical legend wraps into; PDF dimensions scale automatically to fit. When group_by_vars has multiple variables, pass a vector aligned positionally (e.g. c(3, 1)) or named by variable (e.g. c(seurat_clusters = 3, Diagnosis = 1)) to set a different row count per variable; a single value applies to all. Default 3.

legend.side

Character. Where to place the legend panel: "bottom" (default), "top", "left", or "right".

legend.direction

Character. Internal layout of legend entries: "horizontal" (default, entries in rows) or "vertical" (entries stacked in one column).

join_plots

Logical. When group_by_vars has more than one variable, combine all per-variable figures into a single page instead of one page each. Default FALSE.

join_nrow, join_ncol

Integer or NULL. Grid layout for join_plots. NULL auto-arranges into a near-square grid.

output_dir

Character or NULL. PDF output directory. When NULL the plot is printed to the active device and returned invisibly.

rowannsize

Numeric. Font size for the row-group annotation label. Default 16.

imgalpha

Numeric. Tissue image transparency. Default 1.

alpha

Numeric. Spot transparency. Default 1.

object_name

Character. Label appended to PDF filenames. Default "".

group.by

Character vector. Preferred alias for group_by_vars.

cluster_colors

Named character vector. Deprecated alias for colors.

subset_name

Character. Optional second label appended to PDF filenames after object_name. Default "".

file_name

Character or NULL. Base name (no extension) for the saved PDF. NULL (default) auto-deduces from object_name, subset_name, row.by, and the grouping variable(s).

width, height

Numeric or NULL. Override the auto-calculated PDF dimensions in inches. NULL (default) auto-sizes to fit the image grid and legend.

timestamp

Logical. When TRUE, append a _YYYYMMDD-HHMMSS stamp to the saved file name so repeated runs are versioned instead of overwriting the previous PDF. Default FALSE.

Value

Invisibly returns the plot, or a named list of plots when join_plots = FALSE and multiple variables are supplied.

Functions

  • GenerateSpatialDimMaps(): Long-form alias.