spatGenePlot3D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L8734


Visualize cells and gene expression according to spatial coordinates

Usage#

spatGenePlot3D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  spat_loc_name = NULL,
  expression_values = c("normalized", "scaled", "custom"),
  genes,
  show_network = FALSE,
  network_color = NULL,
  spatial_network_name = "Delaunay_network",
  edge_alpha = NULL,
  cluster_column = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 1,
  genes_high_color = NULL,
  genes_mid_color = "white",
  genes_low_color = "blue",
  show_grid = FALSE,
  spatial_grid_name = "spatial_grid",
  point_size = 2,
  show_legend = TRUE,
  axis_scale = c("cube", "real", "custom"),
  custom_ratio = NULL,
  x_ticks = NULL,
  y_ticks = NULL,
  z_ticks = NULL,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatGenePlot3D"
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

spat_loc_name

name of spatial locations to use

expression_values

gene expression values to use

genes

genes to show

show_network

show underlying spatial network

network_color

color of spatial network

spatial_network_name

name of spatial network to use

edge_alpha

alpha of edges

cluster_column

cluster column to select groups

select_cell_groups

select subset of cells/clusters based on cell_color parameter

select_cells

select subset of cells based on cell IDs

show_other_cells

display not selected cells

other_cell_color

color of not selected cells

other_point_size

size of not selected cells

genes_high_color

color represents high gene expression

genes_mid_color

color represents middle gene expression

genes_low_color

color represents low gene expression

show_grid

show spatial grid

spatial_grid_name

name of spatial grid to use

point_size

size of point (cell)

show_legend

show legend

axis_scale

the way to scale the axis

custom_ratio

customize the scale of the plot

x_ticks

set the number of ticks on the x-axis

y_ticks

set the number of ticks on the y-axis

z_ticks

set the number of ticks on the z-axis

show_plot

show plots

return_plot

return ggplot object

save_plot

directly save the plot [boolean]

save_param

list of saving parameters, see `showSaveP arameters <#showsaveparameters>`__

default_save_name

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

Details#

Description of parameters.

Value#

ggplot

Seealso#

Other spatial gene expression visualizations: `spatGenePlot2D <#spatgeneplot2d>`__ , `spatGenePlot <#spatgeneplot>`__