Feature2Plotly3D: Feature2Plotly3D

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

Description

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

Usage

Feature2Plotly3D(object, reduction = "umap", feature_1 = NULL,
  feature_2 = NULL, assay_1 = NULL, assay_2 = NULL,
  colors_1 = "Reds", colors_2 = "Blues", dim_1 = 1, dim_2 = 2,
  dim_3 = 3, bins = 10, return = FALSE, pt_scale = 0.5,
  pt_shape = "circle", opacity = 1, plot_height = "750",
  plot_width = "750", pt_info = NULL, legend = TRUE,
  legend_font_size = 12, plot_grid = FALSE, plot_axes = FALSE)

Arguments

object	Seurat object
reduction	Dimensional reduction to display. Default: 'umap'
feature_1	First feature values to display. Works with anything Seurat::FetchData can retrieve.
feature_2	Second feature values to display.
assay_1	Assay to pull values from for feature_1. Default: NULL
assay_2	Assay to pull values from for feature_2. Default: NULL
colors_1	Colors to use to display values for feature_1. Default: "Reds"
colors_2	Colors to use to display values for feature_2. Default: "Blues"
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
bins	Number of bins to use in dividing expression levels.. Default: 10
return	Return the plot object instead of displaying it. Default: FALSE
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
plot_height	Plot height in pixels. Default: 900
plot_width	Plot width in pixels. Default: 900
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

Value

If return is TRUE, a plotly object.

milescsmith/SeuratPlotly documentation built on June 5, 2019, 1:16 a.m.