cellProximityVisPlot#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_interaction_visuals.R#L962

Description#

Visualize cell-cell interactions according to spatial coordinates

Usage#

cellProximityVisPlot(
  gobject,
  interaction_name = NULL,
  cluster_column = NULL,
  sdimx = NULL,
  sdimy = NULL,
  sdimz = NULL,
  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,
  axis_scale = c("cube", "real", "custom"),
  custom_ratio = NULL,
  x_ticks = NULL,
  y_ticks = NULL,
  z_ticks = NULL,
  plot_method = c("ggplot", "plotly"),
  ...
)

Arguments#

Argument

Description

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’)

sdimz

z-axis dimension name (default = ‘sdimz’)

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

show not selected cells

show_network

show underlying spatial network

show_other_network

show underlying spatial network of other 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

alpha of other points

point_other_border_col

border color of other points

point_other_border_stroke

stroke size of other points

axis_scale

scale of axis

custom_ratio

custom ratio of scales

x_ticks

x ticks

y_ticks

y ticks

z_ticks

z ticks

plot_method

method to plot

list()

additional parameters

Details#

Description of parameters.

Value#

ggplot or plotly