Plot Gene Expression Along Distance from Niche Center

Visualizes gene expression patterns as a function of distance from niche centers, with optional smoothing and scaling.

Usage

Plot_DistLine_Exp(
  STID_obj = NULL,
  loop_id = "LoopAllSamp",
  meta_key = NULL,
  facet_grpnm = NULL,
  assay_id = "Spatial",
  layer_id = "data",
  features = NULL,
  feature_colnm = NULL,
  smooth_method = "gam",
  exp_scale = TRUE,
  distance_scale = TRUE,
  linewidth = 1,
  ncol = 4,
  col = COLOR_LIST[["PALETTE_WHITE_BG"]]
)

Arguments

STID_obj

An STID object containing niche analysis results

loop_id

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

meta_key

Character, metadata key containing distance information

facet_grpnm

Character, column name for faceting

assay_id

Character, assay name (default: "Spatial")

layer_id

Character, layer name (default: "data")

features

Character vector, gene names to plot

feature_colnm

Character vector, metadata column names to plot

smooth_method

Character, smoothing method for geom_smooth (default: "gam")

exp_scale

Logical, whether to scale expression values (default: TRUE)

distance_scale

Logical, whether to scale distance values (default: TRUE)

linewidth

Numeric, line width (default: 1)

ncol

Integer, number of facet columns (default: 4)

col

Color palette (default: COLOR_LIST$PALETTE_WHITE_BG)

Value

A ggplot object

Examples

if (FALSE) { # \dontrun{
# Plot gene expression along distance from niche center
Plot_DistLine_Exp(
  STID_obj = STID_obj,
  features = c("gene1", "gene2"),
  meta_key = "M2_NicheDetect_STS_20240101"
)
} # }