plotEmbeddings: Plots Monocle2 cell embedding plots

In KrishnaswamyLab/phemd: Phenotypic EMD for comparison of single-cell samples

Plots Monocle2 cell embedding plots

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

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

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)

KrishnaswamyLab/phemd documentation built on Oct. 2, 2024, 5:10 a.m.