Visualize cells and gene expression according to spatial coordinates
spatGenePlot(...)
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
ggplot
Description of parameters.
spatGenePlot3D
and spatGenePlot2D
Other spatial gene expression visualizations:
spatGenePlot2D()
,
spatGenePlot3D()
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)