STDistance (version 0.6.6)

visualize_spatial_gradient: Visualize spatial network with expression gradient

Description

Visualize spatial network with expression gradient

Usage

visualize_spatial_gradient(
  spatial_data,
  sample,
  gradient_type,
  fixed_type,
  expression_col = "gen2_SPLIz_numeric",
  x_col = "pxl_row_in_fullres",
  y_col = "pxl_col_in_fullres",
  type_col = "Epi_strom",
  fixed_color = "#A9C6D9",
  line_color = "#666666",
  gradient_palette = "C",
  point_size = 1,
  point_alpha = 0.8,
  line_width = 0.3,
  line_alpha = 0.6,
  show_legend = TRUE,
  legend_title = "Expression",
  grid_major_color = "gray90",
  grid_minor_color = "gray95",
  border_color = "black",
  background_color = "white"
)

Value

A ggplot object showing the spatial relationships with expression gradient

Arguments

spatial_data

Spatial coordinates data frame containing cell types and expression values

sample

Sample name in the spatial transcriptome data

gradient_type

Cell type to show with expression gradient coloring

fixed_type

Cell type to show in fixed color (default gray)

expression_col

Column name containing expression values (default "gen2_SPLIz_numeric")

x_col

Column name for x-coordinates (default "pxl_row_in_fullres")

y_col

Column name for y-coordinates (default "pxl_col_in_fullres")

type_col

Column name for cell type information (default "Epi_strom")

fixed_color

Color for the fixed cell type (default "#A9C6D9" - light gray-blue)

line_color

Color for connection lines (default "#666666" - dark gray)

gradient_palette

Color palette for expression gradient (default viridis option "C")

point_size

Size of points (default 1)

point_alpha

Transparency of points (default 0.8)

line_width

Width of connection lines (default 0.3)

line_alpha

Transparency of connection lines (default 0.6)

show_legend

Logical whether to show legend (default TRUE)

legend_title

Title for the legend (default "Expression")

grid_major_color

Color for major grid lines (default "gray90")

grid_minor_color

Color for minor grid lines (default "gray95")

border_color

Color for plot border (default "black")

background_color

Color for plot background (default "white")

Examples

visualize_spatial_gradient(spatial_data = posi,
                           sample="SP8",
                           gradient_type = "Epithelial_cells_A",
                           fixed_type = "Macrophage",
                           expression_col = "gen2_SPLIz_numeric",
                           type_col = "celltype_ABCDepi",
                           legend_title = "Expression",
                           background_color = "white")