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Detect infection spots based on individual gene expression

Source: R/SpotDetect.R
SpotDetect_Gene.Rd

This function identifies positive spots based on expression thresholds for individual genes. It can apply spatial smoothing and generates visualization of gene expression patterns.

Usage

SpotDetect_Gene(
  STID_obj = NULL,
  features = NULL,
  feature_colnm = NULL,
  loop_id = "LoopAllSamp",
  assay_id = "Spatial",
  layer_id = "counts",
  PosThres_prob = 0,
  PosThres_count = 0,
  PosThres_gene = 1,
  col = COLOR_DIS_CON,
  pt_size = 0.5,
  vmin = NULL,
  vmax = "p99",
  black_bg = FALSE,
  plot_method = "merge",
  blur_method = NULL,
  blur_n = 1,
  blur_sigma = 0.25,
  description = NULL,
  grp_nm = NULL,
  dir_nm = "M1_SpotDetect_Gene"
)

Arguments

STID_obj

An STID object containing spatial transcriptomics data

features

Character vector of gene names to analyze

feature_colnm

Character, column name in metadata containing pre-computed features

loop_id

Character, sample grouping identifier (default: "LoopAllSamp")

assay_id

Character, name of the assay to use (default: "Spatial")

layer_id

Character, name of the layer/data slot to use (default: "counts")

PosThres_prob

Numeric, probability threshold (0-1) for positive detection (default: 0)

PosThres_count

Numeric, absolute count threshold for positive detection (default: 0)

PosThres_gene

Numeric, gene number threshold (default: 1)

col

Color palette for visualization (default: COLOR_DIS_CON)

pt_size

Numeric, point size in spatial plots (default: 0.5)

vmin

Numeric or character, minimum value for color scale (default: NULL)

vmax

Numeric or character, maximum value for color scale (default: "p99")

black_bg

Logical, whether to use black background in plots (default: FALSE)

plot_method

Character, plotting mode - "merge" or "single" (default: "merge")

blur_method

Character, spatial smoothing method - "isoblur" or "medianblur" (default: NULL)

blur_n

Numeric, number of iterations for median blur (default: 1)

blur_sigma

Numeric, sigma parameter for isoblur (default: 0.25)

description

Character, description of the analysis (default: NULL)

grp_nm

Character, group name for output organization (default: NULL)

dir_nm

Character, directory name for output (default: "M1_SpotDetect_Gene")

Value

Returns the modified STID object with added metadata containing gene expression labels and thresholds

Examples

if (FALSE) { # \dontrun{
# Detect spots based on pathogen gene expression
STID_obj <- SpotDetect_Gene(
  STID_obj = STID_object,
  features = c("geneA", "geneB", "geneC"),
  PosThres_prob = 0.95,
  PosThres_count = 1,
  plot_method = "merge"
)
} # }