Visualize cells according to spatial AND dimension reduction coordinates in ggplot mode
Usage
spatDimFeatPlot3D(
gobject,
feat_type = NULL,
spat_unit = NULL,
spat_loc_name = NULL,
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 = TRUE,
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 = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "spatDimFeatPlot3D"
)
spatDimGenePlot3D(...)Arguments
- gobject
giotto object
- feat_type
feature type (e.g. "rna", "dna", "protein")
- spat_unit
spatial unit (e.g. "cell")
- spat_loc_name
name of spatial locations to use
- 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
- spatial_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
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
#>
#> no external python path or giotto
#> environment was specified, will check if a
#> default python path is available
#>
#> A default python path was found: /usr/bin/python3 and will be used
#> If this is not the correct python path, either
#>
#> 1. use installGiottoEnvironment() to install
#> a local miniconda python environment along with required modules
#>
#> 2. provide an existing python path to
#> python_path to use your own python path which has all modules
#> installed
#> Set options("giotto.use_conda" = FALSE) if
#> python functionalities are not needed
spatDimFeatPlot3D(g, genes = "Slc17a7")
#> Warning: 'layout' objects don't have these attributes: 'NA'
#> Valid attributes include:
#> '_deprecated', 'activeshape', 'annotations', 'autosize', 'autotypenumbers', 'calendar', 'clickmode', 'coloraxis', 'colorscale', 'colorway', 'computed', 'datarevision', 'dragmode', 'editrevision', 'editType', 'font', 'geo', 'grid', 'height', 'hidesources', 'hoverdistance', 'hoverlabel', 'hovermode', 'images', 'legend', 'mapbox', 'margin', 'meta', 'metasrc', 'modebar', 'newshape', 'paper_bgcolor', 'plot_bgcolor', 'polar', 'scene', 'selectdirection', 'selectionrevision', 'separators', 'shapes', 'showlegend', 'sliders', 'smith', 'spikedistance', 'template', 'ternary', 'title', 'transition', 'uirevision', 'uniformtext', 'updatemenus', 'width', 'xaxis', 'yaxis', 'barmode', 'bargap', 'mapType'