spatDimGenePlot3D

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

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

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
default_save_name: default save name for saving, don't change, change save_name in save_param

Value

plotly

Details

Description of parameters.

Arguments

Value

Details

See also