A basic function for pseudotissue visualization — visualized

Adapted function from Giotto package Dries et al, 2021, rewrite for use in scdrake package in a SingleCellExperiment object

Usage

visualized_spots(
  sce,
  sdimx = "Dims_x",
  sdimy = "Dims_y",
  spat_enr_names = NULL,
  cell_color = NULL,
  color_as_factor = F,
  cell_color_code = NULL,
  cell_color_gradient = c("navy", "lightcyan", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  select_cells = NULL,
  point_shape = c("border", "no_border"),
  point_size = 3,
  point_alpha = 1,
  point_border_col = "black",
  point_border_stroke = 0.1,
  label_size = 4,
  label_fontface = "bold",
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 1,
  other_cells_alpha = 0.1,
  coord_fix_ratio = NULL,
  title = NULL,
  show_legend = T,
  legend_text = 8,
  legend_symbol_size = 1,
  background_color = "white",
  axis_text = 8,
  axis_title = 8
)

Arguments

sce: A SingleCellExperiment object.
cell_color, color_as_factor, cell_color_code, ...: Passed to ggplot2 object in plot_spat_point_layer_ggplot function

Value

A ggplot2 object.