plot_spat_point_layer_ggplot: A function for pseudotissue visualization

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

A function for pseudotissue visualization

Description

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

Usage

plot_spat_point_layer_ggplot(
  ggobject,
  sdimx = NULL,
  sdimy = NULL,
  cell_locations_metadata_selected,
  cell_locations_metadata_other,
  cell_color = NULL,
  color_as_factor = T,
  cell_color_code = NULL,
  cell_color_gradient = c("yellow", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  select_cells = NULL,
  point_size = 2,
  point_alpha = 1,
  point_border_col = "lightgrey",
  point_border_stroke = 0.1,
  label_size = 4,
  label_fontface = "bold",
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 1,
  show_legend = TRUE
)

Arguments

ggobject	An inheriated object from visualized_spots.
cell_locations_metadata_selected, cell_locations_metadata_other, cell_color, ...	Inheriated, passed to ggplot2 object.

Value

A ggplot2 object.

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.