Visualize cells according to dimension reduction coordinates
dimPlot3D(
gobject,
dim_reduction_to_use = "umap",
dim_reduction_name = "umap",
dim1_to_use = 1,
dim2_to_use = 2,
dim3_to_use = 3,
spat_enr_names = NULL,
select_cell_groups = NULL,
select_cells = NULL,
show_other_cells = T,
other_cell_color = "lightgrey",
other_point_size = 2,
show_NN_network = F,
nn_network_to_use = "sNN",
network_name = "sNN.pca",
color_as_factor = T,
cell_color = NULL,
cell_color_code = NULL,
show_cluster_center = F,
show_center_label = T,
center_point_size = 4,
label_size = 4,
edge_alpha = NULL,
point_size = 3,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "dim3D"
)
giotto object
dimension reduction to use
dimension reduction name
dimension to use on x-axis
dimension to use on y-axis
dimension to use on z-axis
names of spatial enrichment results to include
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
show underlying NN network
type of NN network to use (kNN vs sNN)
name of NN network to use, if show_NN_network = TRUE
convert color column to factor
color for cells (see details)
named vector with colors
plot center of selected clusters
plot label of selected clusters
size of center points
size of labels
column to use for alpha of the edges
size of point (cell)
show plot
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
plotly
Description of parameters.
Other reduced dimension visualizations:
dimPlot2D()
,
dimPlot()
,
plotPCA_2D()
,
plotPCA_3D()
,
plotPCA()
,
plotTSNE_2D()
,
plotTSNE_3D()
,
plotTSNE()
,
plotUMAP_2D()
,
plotUMAP_3D()
,
plotUMAP()