Visualize cells and gene expression according to spatial coordinates

spatGenePlot(...)

Arguments

...

Arguments passed on to spatGenePlot2D

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')

expression_values

gene expression values to use

genes

genes to show

cell_color_gradient

vector with 3 colors for numeric data

gradient_midpoint

midpoint for color gradient

gradient_limits

vector with lower and upper limits

show_network

show underlying spatial network

network_color

color of spatial network

spatial_network_name

name of spatial network to use

edge_alpha

alpha of edge

show_grid

show spatial grid

grid_color

color of spatial grid

spatial_grid_name

name of spatial grid to use

midpoint

expression midpoint

scale_alpha_with_expression

scale expression with ggplot alpha parameter

point_shape

shape of points (border, no_border or voronoi)

point_size

size of point (cell)

point_alpha

transparancy of points

point_border_col

color of border around points

point_border_stroke

stroke size of border around points

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_legend

show legend

legend_text

size of legend text

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

show_plot

show plots

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

spatGenePlot3D and spatGenePlot2D

Other spatial gene expression visualizations: spatGenePlot2D(), spatGenePlot3D()

Examples

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1:2]
spatGenePlot(mini_giotto_single_cell, genes = selected_genes, point_size = 3)