Visualize cells according to spatial coordinates

spatCellPlot(...)

Arguments

...

Arguments passed on to spatCellPlot2D

gobject

giotto object

show_image

show a tissue background image

gimage

a giotto image

image_name

name of a giotto image

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_annotation_values

numeric cell annotation columns

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

transparancy of spatial points

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

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 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

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

ggplot

Details

Description of parameters.

See also

Other spatial cell annotation visualizations: spatCellPlot2D()

Examples

data(mini_giotto_single_cell)

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

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

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