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.

See also

Other spatial and dimension reduction gene expression visualizations: spatDimGenePlot2D(), spatDimGenePlot()