4-column master gene map: UMAP clusters + UMAP expression + Spatial clusters + Spatial expression

For each gene, generates one PDF with one row per spatial image, and four columns: UMAP colored by clusters, UMAP colored by gene expression, spatial plot colored by clusters, and spatial plot colored by gene expression. A single pair of legends (categorical + continuous) is attached to the right.

Usage

PlotMasterMaps(
  seurat_object,
  features,
  imgalpha = 1,
  alpha = 1,
  group.by = "seurat_clusters",
  images_to_plot = NULL,
  remove_outliers = FALSE,
  outlier_prob = 0.01,
  size_override = NULL,
  calcptsizesc = 100,
  colors = NULL,
  gene_colors = c("#053061", "#2166AC", "#D1E5F0", "#FDDBC7", "#F4A582", "#D6604D",
    "#B2182B", "#67001F"),
  legend.side = "right",
  legend.direction = "vertical",
  output_dir = NULL,
  object_name = "",
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE,
  cluster_col = NULL,
  cluster_colors = NULL
)

GenerateMasterGeneMaps(
  seurat_object,
  features,
  imgalpha = 1,
  alpha = 1,
  group.by = "seurat_clusters",
  images_to_plot = NULL,
  remove_outliers = FALSE,
  outlier_prob = 0.01,
  size_override = NULL,
  calcptsizesc = 100,
  colors = NULL,
  gene_colors = c("#053061", "#2166AC", "#D1E5F0", "#FDDBC7", "#F4A582", "#D6604D",
    "#B2182B", "#67001F"),
  legend.side = "right",
  legend.direction = "vertical",
  output_dir = NULL,
  object_name = "",
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE,
  cluster_col = NULL,
  cluster_colors = NULL
)

Arguments

seurat_object: A Seurat object with both "umap" reduction and spatial images.
features: Character vector of gene names.
imgalpha: Numeric. Tissue image transparency. Default 1.
alpha: Numeric. Spot transparency. Default 1.
group.by: Character (or vector). Metadata column(s) for cluster coloring. Default "seurat_clusters". When a vector is supplied, the function recurses and produces one PDF set per variable.
images_to_plot: Character vector or NULL. Images to include.
remove_outliers: Logical. Default FALSE.
outlier_prob: Numeric. Default 0.01.
size_override: Scalar or named numeric list. A plain number applies to all images; a named list applies per image.
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 group.by levels. NULL auto-resolves from PrepObject or Nour_pal.
gene_colors: Character vector. Gradient for gene expression.
legend.side: Character. Where to place the paired legends: "right" (default, stacked vertically) or "bottom" (side by side).
legend.direction: Character. Internal layout of the categorical cluster legend: "vertical" (default) or "horizontal".
output_dir: Character or NULL. Output directory for PDFs. When NULL the plot is printed to the active device and returned invisibly. Walk-up from PrepObject applies when omitted entirely.
object_name: Character. Label for 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, the gene, and group.by.
width, height: Numeric or NULL. Override the auto-calculated PDF dimensions in inches. NULL (default) auto-sizes to fit the row 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.
cluster_col: Deprecated alias for group.by.
cluster_colors: Deprecated alias for colors.

Value

Invisibly returns the last assembled plot when output_dir = NULL; otherwise writes PDFs and returns NULL invisibly.

Details

Accepts a vector for group.by: one PDF set is produced per variable.

Functions

GenerateMasterGeneMaps(): Long-form alias.