This function generates spatial visualizations with discrete or continuous coloring. Can be used directly with an STID object or with a custom data frame.
Usage
Plot_Spatial(
STID_obj = NULL,
meta_key = NULL,
plot_data = NULL,
x_colnm = NULL,
y_colnm = NULL,
group_by = NULL,
facet_grpnm = NULL,
datatype = "discrete",
col = COLOR_DIS_CON,
pt_size = 1.1,
vmin = NULL,
vmax = "p99",
title = NULL,
subtitle = NULL,
black_bg = FALSE
)Arguments
- STID_obj
An STID object (optional if plot_data provided)
- meta_key
Character, metadata key to use (default: NULL)
- plot_data
Data frame containing plotting data (optional if STID_obj provided)
- x_colnm
Character, column name for x coordinates
- y_colnm
Character, column name for y coordinates
- group_by
Character, column name for grouping/coloring variable
- facet_grpnm
Character, column name for faceting (default: NULL)
- datatype
Character, data type - "discrete" or "continuous" (default: "discrete")
- col
Color palette for visualization (default: COLOR_DIS_CON)
- pt_size
Numeric, point size (default: 1.1)
- vmin
Numeric or character, minimum value for color scale (default: NULL)
- vmax
Numeric or character, maximum value for color scale (default: "p99")
- title
Character, plot title (default: NULL)
- subtitle
Character, plot subtitle (default: NULL)
- black_bg
Logical, whether to use black background (default: FALSE)
Examples
if (FALSE) { # \dontrun{
# Create spatial plot from STID object
p <- Plot_Spatial(
STID_obj = STID_object,
group_by = "Pathogen_Score",
datatype = "continuous",
black_bg = TRUE
)
# Create spatial plot from custom data frame
p <- Plot_Spatial(
plot_data = my_data,
x_colnm = "x_coord",
y_colnm = "y_coord",
group_by = "cell_type",
datatype = "discrete"
)
} # }