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Batch spatial feature plots for genes and/or metadata columns

PlotSpatialFeaturePlots.Rd

Loops over features (gene names or numeric metadata columns) and produces Seurat::SpatialFeaturePlot() panels for each image in the object. A shared color scale (0 → max) is applied across all images for the same feature. Panels are arranged in a grid and a shared legend is attached.

Usage

PlotSpatialFeaturePlots(
  seurat_object,
  features,
  layout_method = "auto",
  row.by = NULL,
  images_to_plot = NULL,
  remove_outliers = FALSE,
  outlier_prob = 0.01,
  size_override = NULL,
  colors = c("#053061", "#2166AC", "#D1E5F0", "#FDDBC7", "#F4A582", "#D6604D", "#B2182B",
    "#67001F"),
  na.value = "transparent",
  calcptsizesc = 100,
  legend.side = "right",
  legend.direction = "vertical",
  join_plots = FALSE,
  join_nrow = NULL,
  join_ncol = NULL,
  output_dir = NULL,
  object_name = "",
  image.alpha = 0.5,
  alpha = 1,
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE
)

GenerateSpatialFeatureMaps(
  seurat_object,
  features,
  layout_method = "auto",
  row.by = NULL,
  images_to_plot = NULL,
  remove_outliers = FALSE,
  outlier_prob = 0.01,
  size_override = NULL,
  colors = c("#053061", "#2166AC", "#D1E5F0", "#FDDBC7", "#F4A582", "#D6604D", "#B2182B",
    "#67001F"),
  na.value = "transparent",
  calcptsizesc = 100,
  legend.side = "right",
  legend.direction = "vertical",
  join_plots = FALSE,
  join_nrow = NULL,
  join_ncol = NULL,
  output_dir = NULL,
  object_name = "",
  image.alpha = 0.5,
  alpha = 1,
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE
)

Arguments

seurat_object

A Seurat object with spatial images.

features

Character vector of gene names or numeric metadata column names.

layout_method

Character. "auto" (default) or "metadata".

row.by

Character or NULL. Slide-level metadata column for grouping images into rows (required when layout_method = "metadata").

images_to_plot

Character vector or NULL. Subset of image names to include. NULL uses all images.

remove_outliers

Logical. Crop outlier cells before plotting. Default FALSE.

outlier_prob

Numeric. Quantile to trim when remove_outliers = TRUE. Default 0.01.

size_override

Scalar or named numeric list. A plain number (e.g. size_override = 1.5) applies to all images; a named list applies per image. Overrides auto-sizing.

colors

Character vector. Gradient colors from low to high.

calcptsizesc

Numeric. Scaling constant for auto point-size calculation. Default 100.

legend.side

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

legend.direction

Character. Internal layout of legend entries: "vertical" (default, entries stacked) or "horizontal" (entries arranged in rows). Also controls colorbar orientation.

join_plots

Logical. When features has more than one gene, combine all per-feature figures into a single page/PDF instead of one 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. Output directory for PDFs. Returns last plot when NULL.

object_name

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

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 feature name(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 last plot when output_dir = NULL. When join_plots = TRUE, invisibly returns the combined tiled figure.

Details

Supports two layout modes:

"auto"

Automatic 1- or 2-row grid.

"metadata"

Groups images into rows based on a slide-level metadata variable (row.by). The variable must have a single unique value per image.

Functions

  • GenerateSpatialFeatureMaps(): Long-form alias.