cellProximitySpatPlot2D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L2645

Description#

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

Usage#

cellProximitySpatPlot2D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  spat_loc_name = NULL,
  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#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

spat_loc_name

spatial locations to use

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_f unction <#allplotssavefunction>`__

default_save_name

default save name for saving, don’t change, change save_name in save_param

Details#

Description of parameters.

Value#

ggplot