`spatDimGenePlot3D`¶

spatDimGenePlot3D

Description¶

Visualize cells according to spatial AND dimension reduction coordinates in ggplot mode

Usage¶

spatDimGenePlot3D(
  gobject,
  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 = T,
  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 = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "spatDimGenePlot3D"
)

Arguments¶

Argument	Description
`gobject`	giotto object
`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`	show plots
`return_plot`	return plotly object
`save_plot`	directly save the plot [boolean]
`save_param`	list of saving parameters, see ``showSaveParameters` <#showsaveparameters>`_
`default_save_name`	default save name for saving, don’t change, change save_name in save_param

Details¶

Description of parameters.

Value¶

plotly

Seealso¶

Other spatial and dimension reduction gene expression visualizations:: ``spatDimGenePlot2D` <#spatdimgeneplot2d>`_ , ``spatDimGenePlot` <#spatdimgeneplot>`_