spatDimCellPlot2D

spatDimCellPlot2D

Description

Visualize numerical features of cells according to spatial AND dimension reduction coordinates in 2D

Usage

spatDimCellPlot2D(
  gobject,
  show_image = F,
  gimage = NULL,
  image_name = "image",
  plot_alignment = c("vertical", "horizontal"),
  spat_enr_names = NULL,
  cell_annotation_values = NULL,
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  dim1_to_use = 1,
  dim2_to_use = 2,
  sdimx = "sdimx",
  sdimy = "sdimy",
  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 = "black",
  spat_center_point_border_stroke = 0.1,
  spat_label_size = 4,
  spat_label_fontface = "bold",
  show_NN_network = F,
  nn_network_to_use = "sNN",
  nn_network_name = "sNN.pca",
  dim_edge_alpha = 0.5,
  spat_show_network = F,
  spatial_network_name = "Delaunay_network",
  spat_network_color = "red",
  spat_network_alpha = 0.5,
  spat_show_grid = F,
  spatial_grid_name = "spatial_grid",
  spat_grid_color = "green",
  show_other_cells = TRUE,
  other_cell_color = "grey",
  dim_other_point_size = 0.5,
  spat_other_point_size = 0.5,
  spat_other_cells_alpha = 0.5,
  show_legend = T,
  legend_text = 8,
  legend_symbol_size = 1,
  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,
  coord_fix_ratio = NULL,
  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 = "spatDimCellPlot2D"
)

Arguments

Argument	Description
gobject	giotto object
show_image	show a tissue background image
gimage	a giotto image
image_name	name of a giotto image
plot_alignment	direction to align plot
spat_enr_names	names of spatial enrichment results to include
cell_annotation_values	numeric cell annotation columns
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
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	dim reduction points with border or not (border or no_border)
dim_point_size	size of points in dim. reduction space
dim_point_alpha	transparancy of dim. reduction points
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 spatial center points
spat_center_point_border_col	border color of the spatial center points
spat_center_point_border_stroke	stroke size of the 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)
nn_network_name	name of NN network to use, if show_NN_network = TRUE
dim_edge_alpha	column to use for alpha of the edges
spat_show_network	show spatial network
spatial_network_name	name of spatial network to use
spat_network_color	color of spatial network
spat_network_alpha	alpha of spatial network
spat_show_grid	show spatial grid
spatial_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
show_legend	show legend
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
coord_fix_ratio	ratio for coordinates
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 ``showSaveParameters` <#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 and dimension reduction cell annotation visualizations:

``spatDimCellPlot` <#spatdimcellplot>`_

Examples

data(mini_giotto_single_cell)

# combine all metadata
combineMetadata(mini_giotto_single_cell, spat_enr_names = 'cluster_metagene')

# visualize total expression information
spatDimCellPlot2D(mini_giotto_single_cell, cell_annotation_values = 'total_expr')

# visualize enrichment results
spatDimCellPlot2D(mini_giotto_single_cell,
spat_enr_names = 'cluster_metagene',
cell_annotation_values = c('1','2'))