Visualize Cells By Spatial Coordinates¶

spatPlo2D()

Visualize cells according to spatial coordinates.

spatPlot2D(
    gobject,
    show_image = F,
    gimage = NULL,
    image_name = "image",
    group_by = NULL,
    group_by_subset = 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 = NULL,
    title = NULL,
    show_legend = T,
    legend_text = 8,
    legend_symbol_size = 1,
    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¶

gobject	giotto object
show_image	show a tissue background image
gimage	a giotto image
image_name	name of a giotto image
group_by	create multiple plots based on cell annotation column
group_by_subset	subset the group_by factor column
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	transparency 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
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 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
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()
default_save_name	default save name for saving, don’t change, change save_name in save_param

Value¶

A ggplot.

Details¶

Description of parameters …

See dimPlot2D() and dimPlot3D() for 3D plot information.

Examples¶

data(mini_giotto_single_cell)
spatPlot(mini_giotto_single_cell)

spatPlot(mini_giotto_single_cell, cell_color = 'cell_types', point_size = 3)