spatDimPlot2D

View Source Code

Last Updated: Mar 11, 2023

Description

Visualize cells according to spatial AND dimension reduction coordinates 2D

Usage

spatDimPlot2D(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  show_image = F,
  gimage = NULL,
  image_name = NULL,
  largeImage_name = NULL,
  spat_loc_name = NULL,
  plot_alignment = c("vertical", "horizontal"),
  dim_reduction_to_use = "umap",
  dim_reduction_name = NULL,
  dim1_to_use = 1,
  dim2_to_use = 2,
  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,
  dim_point_shape = c("border", "no_border"),
  dim_point_size = 1,
  dim_point_alpha = 1,
  dim_point_border_col = "black",
  dim_point_border_stroke = 0.1,
  spat_point_shape = c("border", "no_border", "voronoi"),
  spat_point_size = 1,
  spat_point_alpha = 1,
  spat_point_border_col = "black",
  spat_point_border_stroke = 0.1,
  dim_show_cluster_center = F,
  dim_show_center_label = T,
  dim_center_point_size = 4,
  dim_center_point_border_col = "black",
  dim_center_point_border_stroke = 0.1,
  dim_label_size = 4,
  dim_label_fontface = "bold",
  spat_show_cluster_center = F,
  spat_show_center_label = F,
  spat_center_point_size = 4,
  spat_center_point_border_col = "blue",
  spat_center_point_border_stroke = 0.1,
  spat_label_size = 4,
  spat_label_fontface = "bold",
  show_NN_network = F,
  nn_network_to_use = "sNN",
  network_name = "sNN.pca",
  nn_network_alpha = 0.05,
  show_spatial_network = F,
  spat_network_name = "Delaunay_network",
  spat_network_color = "blue",
  spat_network_alpha = 0.5,
  show_spatial_grid = F,
  spat_grid_name = "spatial_grid",
  spat_grid_color = "blue",
  show_other_cells = T,
  other_cell_color = "lightgrey",
  dim_other_point_size = 1,
  spat_other_point_size = 1,
  spat_other_cells_alpha = 0.5,
  dim_show_legend = F,
  spat_show_legend = F,
  legend_text = 10,
  legend_symbol_size = 2,
  dim_background_color = "white",
  spat_background_color = "white",
  vor_border_color = "white",
  vor_max_radius = 200,
  vor_alpha = 1,
  axis_text = 8,
  axis_title = 8,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatDimPlot2D"
)

Arguments

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
largeImage_name	name of a giottoLargeImage
spat_loc_name	name of spatial locations
plot_alignment	direction to align plot
dim_reduction_to_use	dimension reduction to use
dim_reduction_name	dimension reduction name
dim1_to_use	dimension to use on x-axis
dim2_to_use	dimension to use on y-axis
sdimx	= spatial dimension to use on x-axis
sdimy	= spatial dimension to use on y-axis
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
dim_point_shape	point with border or not (border or no_border)
dim_point_size	size of points in dim. reduction space
dim_point_alpha	transparancy of point in dim. reduction space
dim_point_border_col	border color of points in dim. reduction space
dim_point_border_stroke	border stroke of points in dim. reduction space
spat_point_shape	shape of points (border, no_border or voronoi)
spat_point_size	size of spatial points
spat_point_alpha	transparancy of spatial points
spat_point_border_col	border color of spatial points
spat_point_border_stroke	border stroke of spatial points
dim_show_cluster_center	show the center of each cluster
dim_show_center_label	provide a label for each cluster
dim_center_point_size	size of the center point
dim_center_point_border_col	border color of center point
``dim_center_point_border_stroke` `	stroke size of center point
dim_label_size	size of the center label
dim_label_fontface	font of the center label
spat_show_cluster_center	show the center of each cluster
spat_show_center_label	provide a label for each cluster
spat_center_point_size	size of the center point
spat_center_point_border_col	border color of spatial center points
``spat_center_point_border_stroke ``	border strike size of spatial center points
spat_label_size	size of the center label
spat_label_fontface	font of the center label
show_NN_network	show underlying NN network
nn_network_to_use	type of NN network to use (kNN vs sNN)
network_name	name of NN network to use, if show_NN_network = TRUE
nn_network_alpha	column to use for alpha of the edges
show_spatial_network	show spatial network
spat_network_name	name of spatial network to use
spat_network_color	color of spatial network
spat_network_alpha	alpha of spatial network
show_spatial_grid	show spatial grid
spat_grid_name	name of spatial grid to use
spat_grid_color	color of spatial grid
show_other_cells	display not selected cells
other_cell_color	color of not selected cells
dim_other_point_size	size of not selected dim cells
spat_other_point_size	size of not selected spat cells
spat_other_cells_alpha	alpha of not selected spat cells
dim_show_legend	show legend of dimension reduction plot
spat_show_legend	show legend of spatial plot
legend_text	size of legend text
legend_symbol_size	size of legend symbols
dim_background_color	background color of points in dim. reduction space
spat_background_color	background color of spatial points
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
show_plot	show plot
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see showSaveParameters
default_save_name	default save name for saving, don’t change, change save_name in save_param

Details

Description of parameters.

Value

ggplot

See Also

spatDimPlot3D

Other spatial and dimension reduction visualizations: spatDimPlot3D(), spatDimPlot()