plotEmbeddings {phemd} | R Documentation |
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.
plotEmbeddings( obj, cell_model = c("monocle2", "seurat", "phate"), cmap = NULL, w = 4, h = 5, pt_sz = 1, ndims = NULL )
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) |
embedCells
and orderCellsMonocle
need to be called before calling this function. Required additional packages: 'RColorBrewer', 'cowplot'
Colormap (vector of colors) used to color Monocle2 cell state embedding
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)