plotPCA_3D

plotPCA_3D

Description

Visualize cells according to 3D PCA dimension reduction

Usage

plotPCA_3D(
  gobject,
  dim_reduction_name = "pca",
  default_save_name = "PCA_3D",
  ...
)

Arguments

Argument	Description
gobject	giotto object
dim_reduction_name	name of PCA
default_save_name	default save name of PCA plot
...	Arguments passed on to ``dimPlot3D` <#dimplot3d>`_ list(“n”, ” “, list(list(list(“spat_unit”)), list(“spatial unit”)), “n”, ” “, list(list(list(“feat_type”)), list(“feature type”)), “n”, ” “, list(list(list(“dim1_to_use”)), list(“dimension to use on x-axis”)), “n”, ” “, list(list(list(“dim2_to_use”)), list(“dimension to use on y-axis”)), “n”, ” “, list(list(list(“dim3_to_use”)), list(“dimension to use on z-axis”)), “n”, ” “, list(list(list(“spat_enr_names”)), list(“names of spatial enrichment results to include”)), “n”, ” “,

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` <#plotpca>`_ , ``plotTSNE_2D` <#plottsne2d>`_ , ``plotTSNE_3D` <#plottsne3d>`_ , ``plotTSNE` <#plottsne>`_ , ``plotUMAP_2D` <#plotumap2d>`_ , ``plotUMAP_3D` <#plotumap3d>`_ , ``plotUMAP` <#plotumap>`_