plotUMAP_3D#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_visuals.R#L7170

Description#

Visualize cells according to dimension reduction coordinates

Usage#

plotUMAP_3D(
  gobject,
  dim_reduction_name = "umap",
  default_save_name = "UMAP_3D",
  ...
)

Arguments#

Argument

Description

gobject

giotto object

dim_reduction_name

name of UMAP

default_save_name

default save name of UMAP plot

...

Arguments passed on to `dimPlot3D <#dimplot3d>`__ list(“?, ? “, list(list(list(?spat_unit?)), list(“spatial unit?)), “?, ? “, list(list(list(?feat_type?)), list(“feature type?)), “?, ? “, list(list(list(?dim1_to_use?)), list(“dimension to use on x-axis?)), “?, ? “, list(list(list(?dim2_to_use?)), list(“dimension to use on y-axis?)), “?, ? “, list(list(list(?dim3_to_use?)), list(“dimension to use on z-axis?)), “?, ? “, list(list(list(?spat_enr_names?)), list(“names of spatial enrichment results to include?)), “?, ? “,

list(list(list("show_NN_network")), list("show underlying NN network")), "\n", "    ", list(list(list("nn_network_to_use")), list("type of NN network to use (kNN vs sNN)")), "\n", "    ", list(list(list("network_name")), list("name of NN network to use, if show_NN_network = TRUE")), "\n", "    ", list(list(list("cell_color")), list("color for cells (see details)")), "\n", "    ", list(list(list("color_as_factor")), list("convert color column to factor")), "\n", "    ", list(list(list("cell_color_code")),
    list("named vector with colors")), "\n", "    ", list(list(list("select_cell_groups")), list("select subset of cells/clusters based on cell_color parameter")), "\n", "    ", list(list(list("select_cells")), list("select subset of cells based on cell IDs")), "\n", "    ", list(list(list("show_other_cells")), list("display not selected cells")), "\n", "    ", list(list(list("other_cell_color")), list("color of not selected cells")), "\n", "    ", list(list(list("other_point_size")), list("size of not selected cells")),
"\n", "    ", list(list(list("show_cluster_center")), list("plot center of selected clusters")), "\n", "    ", list(list(list("show_center_label")), list("plot label of selected clusters")), "\n", "    ", list(list(list("center_point_size")), list("size of center points")), "\n", "    ", list(list(list("label_size")), list("size of labels")), "\n", "    ", list(list(list("edge_alpha")), list("column to use for alpha of the edges")), "\n", "    ", list(list(list("point_size")), list("size of point (cell)")),
"\n", "    ", list(list(list("show_plot")), list("show plot")), "\n", "    ", list(list(list("return_plot")), list("return ggplot object")), "\n", "    ", list(list(list("save_plot")), list("directly save the plot [boolean]")), "\n", "    ", list(list(list("save_param")), list("list of saving parameters, see ", list(list("showSaveParameters")))), "\n", "  ")

Details#

Description of parameters.

Value#

plotly

Seealso#

Other reduced dimension visualizations: `dimPlot2D <#dimplot2d>`__ , `dimPlot3D <#dimplot3d>`__ , `dimPlot <#dimplot>`__ , `plotPCA_2D <#plotpca2d>`__ , `plotPCA_3D <#plotpca3d>`__ , `plotPCA <#plotpca>`__ , `plotTSNE_2D <#plottsne2d>`__ , `plotTSNE_3D <#plottsne3d>`__ , `plotTSNE <#plottsne>`__ , `plotUMAP_2D <#plotumap2d>`__ , `plotUMAP <#plotumap>`__