Visualize cells and gene expression according to dimension reduction coordinates
Usage
dimFeatPlot3D(
gobject,
feat_type = NULL,
spat_unit = NULL,
expression_values = c("normalized", "scaled", "custom"),
genes = NULL,
dim_reduction_to_use = "umap",
dim_reduction_name = "umap",
dim1_to_use = 1,
dim2_to_use = 2,
dim3_to_use = 3,
show_NN_network = FALSE,
nn_network_to_use = "sNN",
network_name = "sNN.pca",
network_color = "lightgray",
cluster_column = NULL,
select_cell_groups = NULL,
select_cells = NULL,
show_other_cells = TRUE,
other_cell_color = "lightgrey",
other_point_size = 1,
edge_alpha = NULL,
point_size = 2,
genes_high_color = NULL,
genes_mid_color = "white",
genes_low_color = "blue",
show_legend = TRUE,
show_plot = NULL,
return_plot = NULL,
save_plot = NULL,
save_param = list(),
default_save_name = "dimFeatPlot3D"
)
dimGenePlot3D(...)Arguments
- gobject
giotto object
- feat_type
feature type (e.g. "rna", "dna", "protein")
- spat_unit
spatial unit (e.g. "cell")
- expression_values
gene expression values to use
- 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
- dim3_to_use
dimension to use on z-axis
- show_NN_network
show underlying NN 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
- network_color
color of NN network
- 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
- edge_alpha
column to use for alpha of the edges
- point_size
size of point (cell)
- genes_high_color
color for high expression levels
- genes_mid_color
color for medium expression levels
- genes_low_color
color for low expression levels
- show_legend
show legend
- 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
dimFeatPlot3D(g, genes = "Slc17a7")
#> Error in dim_dfr[, c(dim1_to_use, dim2_to_use, dim3_to_use)]: subscript out of bounds