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

Description Usage Arguments Value

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

FeaturePlotly(object, feature = NULL, reduction = "umap",
  assay = NULL, slot = NULL, filter_zeros = TRUE, dim_1 = 1,
  dim_2 = 2, pt_scale = 5, pt_shape = "circle", opacity = 1,
  colors_use = "Red", reverse_color_scale = FALSE, bins = 10,
  plot_height = 900, plot_width = 900, plot_title = FALSE,
  pt_info = NULL, legend = TRUE, legend_font_size = 12,
  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
`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
`pt_scale`	Factor by which to multiply the size of the points. Default: 5
`pt_shape`	Shape to use for the points. Default = circle
`opacity`	Transparency level to use for the points, on a 0-1 scale. Default: 1
`colors_use`	Color palette to use. Default: Reds
`reverse_color_scale`	Reverse the color scale. Default = FALSE
`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
`return`	Return the plot dataframe instead of displaying it. Default: FALSE