cluster.dimplot: Plot UMAP dimensional reduction with cluster centers as...

In zdebruine/scNMF: Fast Non-negative matrix factorization toolkit for single cell data

Description

This visualization mode is useful for qualitative assessment of how well a given clustering samples transcriptional space of a given dataset. Note that any ggplot grammar can be applied to the returned plot object.

Usage

cluster.dimplot(
  seuratObj,
  centers = NULL,
  assay = "active.assay",
  slot = "counts",
  ident = "active.ident",
  verbose = TRUE,
  reduction.name = "umap",
  cells.color = "#C0C0C0",
  bubble.color = "#F26815",
  bubble.alpha = 0.8,
  scale.breaks = c(10, 50, 100),
  min.scale.size = 1,
  max.scale.size = 1000,
  bubble.scale = NULL
)

Arguments

seuratObj	A seurat object with UMAP dimensional reduction and cluster idents in the active slot (unless providing centers)
centers	Optionally provide a matrix of averaged centers to be projected onto the UMAP coordinates (returned from average.expression with detail = TRUE)
assay	Assay to use for cluster center averaging (default is the active assay)
slot	Slot in the assay to use for center averaging (default is counts)
verbose	Boolean
reduction.name	If other than "umap", the name of the reduction containing two-dimensional cell embeddings
cells.color	Color code for single cells (default #C0C0C0)
bubble.color	Color code for bubbles as cluster centers (default #F26815)
bubble.alpha	Transparency for bubbles (1 = no transparency, 0 = fully transparent, default = 0.8)
scale.breaks	Legend for bubble size based on number of cells in the cluster center represented by that bubble. Breaks specify what bubble sizes will be shown. Default is c(10,50,100) corresponding to 10, 50, and 100 cells.
min.scale.size	Minimum number of cells a bubble should be scaled to (default is 1). Note that bubbles with fewer than this number of cells will not be displayed.
max.scale.size	Maximum number of cells a bubble should be scaled to (default is 1000). Note that bubbles with more than this number of cells will not be displayed.
bubble.scale	Scale to apply to cluster sizes (i.e. "sqrt", "log2", "log", or default which is NULL for linear scaling)

Value

ggplot object

zdebruine/scNMF documentation built on Jan. 1, 2021, 1:50 p.m.