DimPlotly: DimPlotly

Description Usage Arguments Value

Description

Plot dimensional reduction for a Seurat object

Create a scatterplot of a given dimensional reduction set for a scRNA-seq data object, coloring points by the given grouping_var variable

Usage

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DimPlotly(object, grouping_var = "ident", label = FALSE,
  label_size = 12, show_arrow = FALSE, label_color = "000000",
  return = FALSE, pt_size = 4, pt_shape = "circle", opacity = 0.75,
  reduction = "tsne", dim_1 = 1, dim_2 = 2,
  palette = "default_ucscgb", plot_height = 900, plot_width = 900,
  plot_title = NULL, pt_info = NULL, legend = TRUE,
  legend_font_size = 12)

Arguments

object

scRNA-seq object

grouping_var

Variable by which to group cells. Currently only works with the current ident and column names from meta.data. Default: ident

label

Add a label showing thr group name to the graph. Default: FALSE

label_size

Label font size. Default: 12

show_arrow

Offset the position of the labels and instead point to each group with an arrow. Default: FALSE

label_color

Color for label border and arrow. Need hex value.. Default = '000000'

return

Return the plot object instead of displaying it. Default: FALSE

pt_size

Size of the points in pixels. Default: 2

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

reduction

Dimensional reduction to display. Default: umap

dim_1

Dimension to display on the x-axis. Default: 1

dim_2

Dimension to display on the y-axis. Default: 2

palette

Color palette to use. Must be a palette available in the Paletteer package

plot_height

Plot height in pixels. Default: 900

plot_width

Plot width in pixels. Default: 900

plot_title

Plot title

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

Value

plotly object


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