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Plot multiple features on a single embedding

PlotMultiFeature.Rd

Overlays several genes onto one UMAP / tSNE / PCA plot, coloring cells by which gene they express above a threshold. Three modes are available:

Usage

PlotMultiFeature(
  seurat_object,
  features,
  colors = NULL,
  null_color = "gray70",
  threshold = 0.0125,
  plot_mode = c("gene", "intersection", "scale"),
  pct_cutoff = 0.3,
  intersection_label = "Co-expressing",
  assay = "RNA",
  layer = "data",
  reduction = "umap",
  pt.size = 0.5,
  alpha = 0.9,
  shape = 16,
  title = NULL,
  subtitle = NULL,
  legend_title = "Gene",
  show_legend = TRUE,
  output_dir = NULL,
  object_name = "",
  subset_name = "",
  file_name = NULL,
  width = NULL,
  height = NULL,
  timestamp = FALSE
)

Arguments

seurat_object

A Seurat object (v3 or v5).

features

Character vector of gene names to visualize.

colors

Named or unnamed character vector of colors (one per gene). Auto-filled from Nour_pal("all") for missing entries. If NULL, the full Nour_pal("all") palette is used.

null_color

Color for cells that express no gene above threshold. Default "gray70".

threshold

Numeric scalar, or named numeric vector (names = gene names), giving the minimum expression value for a cell to be considered positive. Default 0.0125.

plot_mode

One of "gene" (default), "intersection", or "scale".

pct_cutoff

For plot_mode = "intersection": the fraction of the gene list a cell must express to count as co-expressing. Default 0.3 (i.e. >= 30% of genes).

intersection_label

Label shown in the legend for co-expressing cells. Default "Co-expressing".

assay

Assay to pull expression from. Default "RNA".

layer

Layer / slot to pull (Seurat v5 layer name or v3 slot name). Default "data".

reduction

Dimensional reduction to use for coordinates. Default "umap".

pt.size

Point size. Default 0.5.

alpha

Point transparency [0, 1]. Default 0.9.

shape

ggplot2 point shape integer. Default 16 (filled circle).

title

Plot title. Default NULL.

subtitle

Plot subtitle. Default NULL.

legend_title

Legend title. Default "Gene".

show_legend

Logical; show color legend? Default TRUE.

output_dir

Directory to save a PDF. If NULL (default) the plot is printed to the active graphics device.

object_name

Optional prefix used when building the output file name.

subset_name

Optional second prefix for the output file name.

file_name

Character or NULL. Base name (no extension) for the saved PDF. NULL (default) auto-deduces from object_name, subset_name, and the first few gene names.

width, height

Numeric or NULL. Override the saved PDF dimensions in inches. NULL (default) uses a fixed 6 x 5 in panel.

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

A ggplot object (invisibly when output_dir is set).

Details

"gene" (default)

Each cell is colored by the last gene in features that it expresses above threshold (later genes overwrite earlier ones for multi-expressing cells). Cells below all thresholds are drawn in null_color.

"intersection"

Cells that express at least pct_cutoff × n_genes genes are highlighted as co-expressing. All others are null_color.

"scale"

Continuous color gradient showing expression level of a single gene (features[1] only).