Feature2Plotly: Feature2Plotly

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 two different features.

Usage

Feature2Plotly(object, feature_1 = NULL, feature_2 = NULL,
  reduction = "umap", assay_1 = NULL, assay_2 = NULL,
  return = FALSE, pt_scale = 1.5, pt_shape = "circle",
  opacity = 0.5, dim_1 = 1, dim_2 = 2, colors_1 = "Reds",
  colors_2 = "Blues", bins = 10, plot_height = "750",
  plot_width = "750", pt_info = NULL, legend = TRUE,
  legend_font_size = 12)

Arguments

object	Seurat object
feature_1	First feature values to display. Works with anything Seurat::FetchData can retrieve.
feature_2	Second feature values to display.
reduction	Dimensional reduction to display. Default: 'umap'
assay_1	Assay to pull values from for feature_1. Default: NULL
assay_2	Assay to pull values from for feature_2. Default: NULL
return	Return the plot dataframe 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
dim_1	Dimension to display on the x-axis. Default: 1
dim_2	Dimension to display on the y-axis. Default: 2
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"
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
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

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