Visualize Cells By Spatial and Dimensional Coordinates Using ggplot¶

spatDimGenePlot3D()

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

spatDimGenePlot3D(
    gobject,
    expression_values = c("normalized", "scaled", "custom"),
    plot_alignment = c("horizontal", "vertical"),
    dim_reduction_to_use = "umap",
    dim_reduction_name = "umap",
    dim1_to_use = 1,
    dim2_to_use = 2,
    dim3_to_use = NULL,
    sdimx = "sdimx",
    sdimy = "sdimy",
    sdimz = "sdimz",
    genes,
    cluster_column = NULL,
    select_cell_groups = NULL,
    select_cells = NULL,
    show_other_cells = T,
    other_cell_color = "lightgrey",
    other_point_size = 1.5,
    show_NN_network = FALSE,
    nn_network_to_use = "sNN",
    nn_network_color = "lightgrey",
    nn_network_alpha = 0.5,
    network_name = "sNN.pca",
    label_size = 16,
    genes_low_color = "blue",
    genes_mid_color = "white",
    genes_high_color = "red",
    dim_point_size = 3,
    show_spatial_network = FALSE,
    spatial_network_name = "Delaunay_network",
    spatial_network_color = "lightgray",
    spatial_network_alpha = 0.5,
    show_spatial_grid = FALSE,
    spatial_grid_name = "spatial_grid",
    spatial_grid_color = NULL,
    spatial_grid_alpha = 0.5,
    spatial_point_size = 3,
    legend_text_size = 12,
    axis_scale = c("cube", "real", "custom"),
    custom_ratio = NULL,
    x_ticks = NULL,
    y_ticks = NULL,
    z_ticks = NULL,
    show_plot = NA,
    return_plot = NA,
    save_plot = NA,
    save_param = list(),
    default_save_name = "spatDimGenePlot3D"
)

Arguments¶

gobject	giotto object
expression_values	gene expression values to use
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
dim3_to_use	dimension to use on z-axis
sdimx	spatial dimension to use on x-axis
sdimy	spatial dimension to use on y-axis
sdimz	spatial dimension to use on z-axis
genes	genes to show
cluster_column	cluster column to select groups
select_cell_groups	select subset of cells/clusters based on cell_color parameter
select_cells	select subset of cells based on cell IDs
show_other_cells	display not selected cells
other_cell_color	color of not selected cells
other_point_size	size of not selected cells
show_NN_network	show underlying NN network
nn_network_to_use	type of NN network to use (kNN vs sNN)
nn_network_color	color of NN network
nn_network_alpha	alpha of NN network
network_name	name of NN network to use, if show_NN_network = TRUE
label_size	size of labels
genes_low_color	color for low expression levels
genes_mid_color	color for medium expression levels
genes_high_color	color for high expression levels
dim_point_size	dim reduction plot: point size
show_spatial_network	show spatial network (boolean)
spatial_network_name	name of spatial network to use
spatial_network_color	color of spatial network
spatial_network_alpha	alpha of spatial network
show_spatial_grid	show spatial grid (boolean)
spatial_grid_name	name of spatial grid to use
spatial_grid_color	color of spatial grid
spatial_grid_alpha	alpha of spatial grid
patial_point_size	spatial plot: point size
legend_text_size	size of legend
axis_scale	the way to scale the axis
custom_ratio	customize the scale of the plot
x_ticks	set the number of ticks on the x-axis
y_ticks	set the number of ticks on the y-axis
z_ticks	set the number of ticks on the z-axis
show_plot	show plots
return_plot	return plotly 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 plotly.

Details¶

Description of parameters.