Visualize cells and gene expression according to dimension reduction coordinates
dimGenePlot3D(
gobject,
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 = F,
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 = T,
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 = T,
show_plot = NA,
return_plot = NA,
save_plot = NA,
save_param = list(),
default_save_name = "dimGenePlot3D"
)giotto object
gene expression values to use
genes to show
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
show underlying NN network
type of NN network to use (kNN vs sNN)
name of NN network to use, if show_NN_network = TRUE
color of NN network
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
column to use for alpha of the edges
size of point (cell)
color for high expression levels
color for medium expression levels
color for low expression levels
show legend
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 dimension reduction gene expression visualizations:
dimGenePlot2D(),
dimGenePlot()