spatDimPlot2D: spatDimPlot2D
In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

spatDimPlot2D

R Documentation

spatDimPlot2D

Description

Visualize cells according to spatial AND dimension reduction coordinates 2D

Usage

spatDimPlot2D(
  gobject,
  show_image = F,
  gimage = NULL,
  image_name = "image",
  plot_alignment = c("vertical", "horizontal"),
  dim_reduction_to_use = "umap",
  dim_reduction_name = "umap",
  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 = 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,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatDimPlot2D"
)

Arguments

`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
`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

Examples


data(mini_giotto_single_cell)

spatDimPlot2D(mini_giotto_single_cell)
spatDimPlot2D(mini_giotto_single_cell, cell_color = 'cell_types',
             spat_point_size = 3, dim_point_size = 3)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.