plotEmbeddings: Plots Monocle2 cell embedding plots

Description Usage Arguments Details Value Examples

View source: R/functions-plotting.R

Description

Takes as input a Phemd object containing either a Monocle2 object or Seurat object (already embedded and ordered) and plots cell embedding plots side by side. Optionally saves to specified folder.

Usage

1
2
3
4
5
6
7
8
9
plotEmbeddings(
  obj,
  cell_model = c("monocle2", "seurat", "phate"),
  cmap = NULL,
  w = 4,
  h = 5,
  pt_sz = 1,
  ndims = NULL
)

Arguments

obj

'Phemd' object containing Monocle 2 object

cell_model

Method by which cell state was modeled (either "monocle2", "seurat", or "phate)

cmap

User-specified colormap to use to color cell state embedding (optional)

w

Width of plot in inches

h

Height of plot in inches

pt_sz

Scalar factor for point size

ndims

Number of dimensions to use for dimensionality reduction in case it hasn't been performed yet (only relevant when using Seurat data as input)

Details

embedCells and orderCellsMonocle need to be called before calling this function. Required additional packages: 'RColorBrewer', 'cowplot'

Value

Colormap (vector of colors) used to color Monocle2 cell state embedding

Examples

1
2
3
4
5
6
my_phemdObj <- createDataObj(all_expn_data, all_genes, as.character(snames_data))
my_phemdObj_lg <- removeTinySamples(my_phemdObj, 10)
my_phemdObj_lg <- aggregateSamples(my_phemdObj_lg, max_cells=1000)
my_phemdObj_monocle <- embedCells(my_phemdObj_lg, data_model='gaussianff', sigma=0.02, maxIter=2)
my_phemdObj_monocle <- orderCellsMonocle(my_phemdObj_monocle)
cmap <- plotEmbeddings(my_phemdObj_monocle)

phemd documentation built on Nov. 8, 2020, 8:15 p.m.