dimGenePlot3D#

Last Updated: Jan 29, 2024

Description#

Visualize cells and gene expression according to dimension reduction coordinates

Usage#

dimGenePlot3D(
  gobject,
  feat_type = NULL,
  spat_unit = NULL,
  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

feat_type

feature type

spat_unit

spatial unit

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()