Visualize Cells By Spatial and Dimensional Coordinates¶

spatDimPlot()

Visualize cells according to spatial AND dimension reduction coordinates in 2D.

spatDimPlot(...)

Arguments¶

…	Arguments passed on to spatDimPlot2D()
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	transparency 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	transparency 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 color for voronoi plot
vor_max_radius	maximum radius for voronoi ‘cells’
vor_alpha	transparency 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`

Value¶

A ggplot.

Details¶

May be used for spatial visualization analysis, particularly for co-expression analysis.

Examples¶

data(mini_giotto_single_cell)
spatDimPlot(mini_giotto_single_cell)

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