Plot interactive 3D spatial plot — plotInteractive3D • Giotto

Plot interactive 3D spatial plot

plotInteractive3D(
  gobject,
  spat_unit = "cell",
  feat_type = "rna",
  cell_color = "leiden_clus",
  cell_color_code = NULL,
  point_size = 0.5,
  width = "100%",
  height = "400px"
)

Arguments

gobject: giotto object
spat_unit: spatial unit (e.g. "cell")
feat_type: feature type (e.g. "rna", "dna", "protein")
cell_color: character. What to color cells by (e.g. metadata col or spatial enrichment col)
cell_color_code: character. discrete colors to use. Palette to use or named vector of colors
point_size: size of point (cell)
width: plot width
height: plot height

Value

data.table with selected cell_IDs, spatial coordinates, and cluster_ID.