This function calculates scores for gene sets using various methods and identifies positive spots based on score thresholds. Supports multiple scoring algorithms including AddModuleScore, AUCell, UCell, and basic statistics.
Usage
SpotDetect_Geneset(
STID_obj = NULL,
geneset_list = NULL,
score_method = "AddModuleScore",
n_iter = 5,
nbin = 10,
seed = 10,
loop_id = "LoopAllSamp",
assay_id = "Spatial",
layer_id = "data",
PosThres_prob = 0,
PosThres_score = 0,
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_Geneset"
)Arguments
- STID_obj
An STID object containing spatial transcriptomics data
- geneset_list
A named list of gene sets for scoring
- score_method
Character, scoring method to use. Options: "AddModuleScore", "AUCell", "UCell", "MeanExp", "SumExp" (default: "AddModuleScore")
- n_iter
Numeric, number of iterations for AddModuleScore (default: 5)
- nbin
Numeric, number of bins for AddModuleScore (default: 10)
- seed
Numeric, random seed for reproducibility (default: 10)
- 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: "data")
- PosThres_prob
Numeric, probability threshold (0-1) for positive detection (default: 0)
- PosThres_score
Numeric, absolute score threshold for positive detection (default: 0)
- 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_Geneset")
Examples
if (FALSE) { # \dontrun{
# Define gene sets
pathogen_genes <- list(
"Virulence" = c("gene1", "gene2", "gene3"),
"Toxin" = c("gene4", "gene5", "gene6")
)
# Detect spots based on gene set scores
STID_obj <- SpotDetect_Geneset(
STID_obj = STID_object,
geneset_list = pathogen_genes,
score_method = "AddModuleScore",
PosThres_prob = 0.95
)
} # }