Visualize cells according to spatial AND dimension reduction coordinates 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

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

Value

ggplot

Details

Description of parameters.

See also

spatDimPlot2D and spatDimPlot3D for 3D visualization.

Other spatial and dimension reduction visualizations: spatDimPlot2D(), spatDimPlot3D()

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)