FeaturePlotly3D: FeaturePlotly3D
In milescsmith/SeuratPlotly: Plotly-based methods for displaying Seurat data

Description Usage Arguments

Create a scatterplot of a given dimensional reduction set for a Seurat object, coloring and sizing points by the expression level of the chosen feature. Requrires a Seurat object with the reduction to be used in the corresponding object@dr slot

FeaturePlotly3D(object, feature = NULL, reduction = "umap",
  assay = NULL, slot = NULL, opacity = 1, filter_zeros = TRUE,
  dim_1 = 1, dim_2 = 2, dim_3 = 3, pt_scale = 0.5,
  pt_shape = "circle", colors_use = "Red", bins = 10,
  plot_height = 900, plot_width = 900, plot_title = FALSE,
  pt_info = NULL, legend = TRUE, legend_font_size = 12,
  plot_grid = FALSE, plot_axes = FALSE, return = FALSE)

`object`	Seurat object
`feature`	Feature values to display. Works with anything `Seurat::FetchData` can retrieve.
`reduction`	Dimensional reduction to display. Default: umap
`assay`	Assay to pull values from for feature. Default: NULL
`slot`	Slot to pull values from for feature. Default: NULL
`opacity`	Transparency level to use for the points, on a 0-1 scale. Default: 1
`filter_zeros`	Remove points with no expression data. Default: TRUE
`dim_1`	Dimension to display on the x-axis. Default: 1
`dim_2`	Dimension to display on the y-axis. Default: 2
`dim_3`	Dimension to display on the z-axis. Default: 3
`pt_scale`	Factor by which to multiply the size of the points. Default: 5
`pt_shape`	Shape to use for the points. Default = circle
`colors_use`	Color palette to use. Accepts palettes available in the paletteer package.. Default: Reds
`bins`	Number of bins to use in dividing expression levels.. Default: 10
`plot_height`	Plot height in pixels. Default: 900
`plot_width`	Plot width in pixels. Default: 900
`plot_title`	Display title with the name of the feature?. Default TRUE
`pt_info`	Meta.data columns to add to the hoverinfo popup. Default: ident
`legend`	Display legend?. Default: TRUE
`legend_font_size`	Legend font size. Default: 12
`plot_grid`	Display the major unit tick marks?. Default: FALSE
`plot_axes`	Display the major x, y, and z axes?. Default: FALSE
`return`	Return the plot object instead of displaying it. Default: FALSE