Visualize Genes By Spatial and Dimension Coordinates Via ggplot

spatDimGenePlot()

Visualize genes according to spatial AND dimension reduction coordinates in ggplot mode.

spatDimGenePlot(...)

Arguments

…	Arguments passed on to spatDimGenePlot2D()
gobject	giotto object
show_image	show a tissue background image
gimage	a giotto image
image_name	name of a Giotto image
expression_values	gene expression values to use
plot_alignment	direction to align plot
genes	genes to show
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
dim_point_shape	dim reduction points with border or not (border or no_border)
dim_point_size	dim reduction plot: point size
dim_point_alpha	transparency of dim. reduction points
dim_point_border_col	color of border around points
dim_point_border_stroke	stroke size of border around points
show_NN_network	show underlying NN network
show_spatial_network	show underlying spatial 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
dim_network_color	color of NN network
dim_edge_alpha	dim reduction plot: column to use for alpha of the edges
scale_alpha_with_expression	scale expression with ggplot alpha parameter
sdimx	spatial x-axis dimension name (default = ‘sdimx’)
sdimy	spatial y-axis dimension name (default = ‘sdimy’)
spatial_network_name	name of spatial network to use
spatial_network_color	color of spatial network
show_spatial_grid	show spatial grid
grid_color	color of spatial grid
spatial_grid_name	name of spatial grid to use
spat_point_shape	spatial points with border or not (border or no_border)
spat_point_size	spatial plot: point size
spat_point_alpha	transparency of spatial points
spat_point_border_col	color of border around points
spat_point_border_stroke	stroke size of border around points
spat_edge_alpha	edge alpha
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_legend	show legend
legend_text	size of legend text
dim_background_color	color of plot background for dimension plot
spat_background_color	color of plot background for spatial plot
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 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

A ggplot.

Details

Description of parameters …

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

See also

For further information see: spatGenePlot3D() and spatGenePlot2D(). For other spatial gene expression visualizations see: spatGenePlot2D(), spatGenePlot3D().

Examples

data(mini_giotto_single_cell)

all_genes = slot(mini_giotto_single_cell, 'gene_ID')
selected_genes = all_genes[1]
spatDimGenePlot(mini_giotto_single_cell, genes = selected_genes,
                dim_point_size = 3, spat_point_size = 3,
                cow_n_col = 1, plot_alignment = 'horizontal')