spatPlot2D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L3181

Description#

Visualize cells according to spatial coordinates

Usage#

spatPlot2D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  show_image = F,
  gimage = NULL,
  image_name = NULL,
  largeImage_name = NULL,
  group_by = NULL,
  group_by_subset = NULL,
  spat_loc_name = NULL,
  sdimx = "sdimx",
  sdimy = "sdimy",
  spat_enr_names = NULL,
  cell_color = NULL,
  color_as_factor = T,
  cell_color_code = NULL,
  cell_color_gradient = c("blue", "white", "red"),
  gradient_midpoint = NULL,
  gradient_limits = NULL,
  select_cell_groups = NULL,
  select_cells = NULL,
  point_shape = c("border", "no_border", "voronoi"),
  point_size = 3,
  point_alpha = 1,
  point_border_col = "black",
  point_border_stroke = 0.1,
  show_cluster_center = F,
  show_center_label = F,
  center_point_size = 4,
  center_point_border_col = "black",
  center_point_border_stroke = 0.1,
  label_size = 4,
  label_fontface = "bold",
  show_network = F,
  spatial_network_name = "Delaunay_network",
  network_color = NULL,
  network_alpha = 1,
  show_grid = F,
  spatial_grid_name = "spatial_grid",
  grid_color = NULL,
  show_other_cells = T,
  other_cell_color = "lightgrey",
  other_point_size = 1,
  other_cells_alpha = 0.1,
  coord_fix_ratio = 1,
  title = NULL,
  show_legend = T,
  legend_text = 10,
  legend_symbol_size = 2,
  background_color = "white",
  vor_border_color = "white",
  vor_max_radius = 200,
  vor_alpha = 1,
  axis_text = 8,
  axis_title = 8,
  cow_n_col = 2,
  cow_rel_h = 1,
  cow_rel_w = 1,
  cow_align = "h",
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatPlot2D"
)

Arguments#

Argument

Description

gobject

giotto object

spat_unit

spatial unit

feat_type

feature type

show_image

show a tissue background image

gimage

a giotto image

image_name

name of a giotto image or multiple images with group_by

largeImage_name

name of a giottoLargeImage or multiple images with group_by

group_by

create multiple plots based on cell annotation column

group_by_subset

subset the group_by factor column

spat_loc_name

name of spatial locations

sdimx

x-axis dimension name (default = ‘sdimx’)

sdimy

y-axis dimension name (default = ‘sdimy’)

spat_enr_names

names of spatial enrichment results to include

cell_color

color for cells (see details)

color_as_factor

convert color column to factor

cell_color_code

named vector with colors

cell_color_gradient

vector with 3 colors for numeric data

gradient_midpoint

midpoint for color gradient

gradient_limits

vector with lower and upper limits

select_cell_groups

select subset of cells/clusters based on cell_color parameter

select_cells

select subset of cells based on cell IDs

point_shape

shape of points (border, no_border or voronoi)

point_size

size of point (cell)

point_alpha

transparancy of point

point_border_col

color of border around points

point_border_stroke

stroke size of border around points

show_cluster_center

plot center of selected clusters

show_center_label

plot label of selected clusters

center_point_size

size of center points

center_point_border_col

border color of center points

` center_point_border_stroke`

border stroke size of center points

label_size

size of labels

label_fontface

font of labels

show_network

show underlying spatial network

spatial_network_name

name of spatial network to use

network_color

color of spatial network

network_alpha

alpha of spatial network

show_grid

show spatial grid

spatial_grid_name

name of spatial grid to use

grid_color

color of spatial grid

show_other_cells

display not selected cells

other_cell_color

color of not selected cells

other_point_size

point size of not selected cells

other_cells_alpha

alpha of not selected cells

coord_fix_ratio

fix ratio between x and y-axis (default = 1)

title

title of plot

show_legend

show legend

legend_text

size of legend text

legend_symbol_size

size of legend symbols

background_color

color of plot background

vor_border_color

border colorr for voronoi plot

vor_max_radius

maximum radius for voronoi ‘cells’

vor_alpha

transparancy of voronoi ‘cells’

axis_text

size of axis text

axis_title

size of axis title

cow_n_col

cowplot param: how many columns

cow_rel_h

cowplot param: relative height

cow_rel_w

cowplot param: relative width

cow_align

cowplot param: how to align

show_plot

show plot

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. coord_fix_ratio: set to NULL to use default ggplot parameters

Value#

ggplot

Seealso#

`spatPlot3D <#spatplot3d>`__

Other spatial visualizations: `spatPlot3D <#spatplot3d>`__ , `spatPlot <#spatplot>`__