cellProximityVisPlot: cellProximityVisPlot

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

cellProximityVisPlot

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

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
...	additional parameters

Details

Description of parameters.

Value

ggplot or plotly

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.