cellProximitySpatPlot2D: cellProximitySpatPlot2D
In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

View source: R/spatial_interaction_visuals.R

cellProximitySpatPlot2D

R Documentation

cellProximitySpatPlot2D

Description

Visualize 2D cell-cell interactions according to spatial coordinates in ggplot mode

Usage

cellProximitySpatPlot2D(
  gobject,
  interaction_name = NULL,
  cluster_column = NULL,
  sdimx = "sdimx",
  sdimy = "sdimy",
  cell_color = NULL,
  cell_color_code = NULL,
  color_as_factor = T,
  show_other_cells = F,
  show_network = F,
  show_other_network = F,
  network_color = NULL,
  spatial_network_name = "Delaunay_network",
  show_grid = F,
  grid_color = NULL,
  spatial_grid_name = "spatial_grid",
  coord_fix_ratio = 1,
  show_legend = T,
  point_size_select = 2,
  point_select_border_col = "black",
  point_select_border_stroke = 0.05,
  point_size_other = 1,
  point_alpha_other = 0.3,
  point_other_border_col = "lightgrey",
  point_other_border_stroke = 0.01,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "cellProximitySpatPlot2D"
)

Arguments

`gobject`	giotto object
`interaction_name`	cell-cell interaction name
`cluster_column`	cluster column with cell clusters
`sdimx`	x-axis dimension name (default = 'sdimx')
`sdimy`	y-axis dimension name (default = 'sdimy')
`cell_color`	color for cells (see details)
`cell_color_code`	named vector with colors
`color_as_factor`	convert color column to factor
`show_other_cells`	decide if show cells not in network
`show_network`	show spatial network of selected cells
`show_other_network`	show spatial network of not selected cells
`network_color`	color of spatial network
`spatial_network_name`	name of spatial network to use
`show_grid`	show spatial grid
`grid_color`	color of spatial grid
`spatial_grid_name`	name of spatial grid to use
`coord_fix_ratio`	fix ratio between x and y-axis
`show_legend`	show legend
`point_size_select`	size of selected points
`point_select_border_col`	border color of selected points
`point_select_border_stroke`	stroke size of selected points
`point_size_other`	size of other points
`point_alpha_other`	opacity of other points
`point_other_border_col`	border color of other points
`point_other_border_stroke`	stroke size of other points
`show_plot`	show plots
`return_plot`	return ggplot object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters from `all_plots_save_function`
`default_save_name`	default save name for saving, don't change, change save_name in save_param