Visualize cells and gene expression according to spatial coordinates
spatGenePlot3D(
gobject,
expression_values = c("normalized", "scaled", "custom"),
genes,
show_network = FALSE,
network_color = NULL,
spatial_network_name = "Delaunay_network",
edge_alpha = NULL,
cluster_column = NULL,
select_cell_groups = NULL,
select_cells = NULL,
show_other_cells = T,
other_cell_color = "lightgrey",
other_point_size = 1,
genes_high_color = NULL,
genes_mid_color = "white",
genes_low_color = "blue",
show_grid = FALSE,
spatial_grid_name = "spatial_grid",
point_size = 2,
show_legend = TRUE,
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 = "spatGenePlot3D"
)giotto object
gene expression values to use
genes to show
show underlying spatial network
color of spatial network
name of spatial network to use
alpha of edges
cluster column to select groups
select subset of cells/clusters based on cell_color parameter
select subset of cells based on cell IDs
display not selected cells
color of not selected cells
size of not selected cells
color represents high gene expression
color represents middle gene expression
color represents low gene expression
show spatial grid
name of spatial grid to use
size of point (cell)
show legend
the way to scale the axis
customize the scale of the plot
set the number of ticks on the x-axis
set the number of ticks on the y-axis
set the number of ticks on the z-axis
show plots
return ggplot object
directly save the plot [boolean]
list of saving parameters, see showSaveParameters
default save name for saving, don't change, change save_name in save_param
ggplot
Description of parameters.
Other spatial gene expression visualizations:
spatGenePlot2D(),
spatGenePlot()