dimGenePlot3D: dimGenePlot3D

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

Visualize cells and gene expression according to dimension reduction coordinates

Usage

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"
)

Arguments

gobject	giotto object
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	show plots
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
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

Details

Description of parameters.

Value

ggplot

See Also

Other dimension reduction gene expression visualizations: dimGenePlot2D(), dimGenePlot()

Examples

    dimGenePlot3D(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.