Visualize cells and gene expression according to spatial coordinates
Usage
spatFeatPlot3D(
gobject,
spat_unit = NULL,
feat_type = NULL,
spat_loc_name = "raw",
expression_values = c("normalized", "scaled", "custom"),
feats,
spat_enr_names = NULL,
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 = FALSE,
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 = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "spatFeatPlot3D",
...
)
spatGenePlot3D(...)Arguments
- gobject
giotto object
- spat_unit
spatial unit (e.g. "cell")
- feat_type
feature type (e.g. "rna", "dna", "protein")
- spat_loc_name
name of spatial locations to use
- expression_values
gene expression values to use
- feats
feats to show
- spat_enr_names
names of spatial enrichment results to include
- 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 edges
- 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
- genes_high_color
color represents high gene expression
- genes_mid_color
color represents middle gene expression
- genes_low_color
color represents low gene expression
- show_grid
show spatial grid
- spatial_grid_name
name of spatial grid to use
- point_size
size of point (cell)
- show_legend
show 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
logical. show plot
- return_plot
logical. return ggplot object
- save_plot
logical. save the plot
- 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
- ...
additional params to pass
Examples
g <- GiottoData::loadGiottoMini("starmap")
#> 1. read Giotto object
#> 2. read Giotto feature information
#> 3. read Giotto spatial information
#> 4. read Giotto image information
#> python already initialized in this session
#> active environment : '/usr/bin/python3'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/bin/python3"
spatFeatPlot3D(g, feats = "Slc17a7")