plotHeatmaps: Plot heatmap of cell subtypes

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

Plot heatmap of cell subtypes

Description

Takes as input a Phemd object containing either a Monocle2, Seurat, or PHATE object (already embedded and clustered) and plots heatmap characterizing cell subtypes

Usage

plotHeatmaps(
  obj,
  cell_model = c("monocle2", "seurat", "phate"),
  selected_genes = NULL,
  w = 8,
  h = 5,
  ...
)

Arguments

obj	'Phemd' object containing cell-state embedding object
cell_model	Method by which cell state was modeled ("monocle2", "seurat", or "phate")
selected_genes	Vector containing gene names to include in heatmap (optional)
w	Width of plot in inches
h	Height of plot in inches
...	Additional parameters to be passed on to pheatmap function

Details

embedCells (and orderCellsMonocle if using Monocle2) need to be called before calling this function. Required additional package: 'pheatmap'

Value

Heatmap containing expression values for each cell subtype. If cell_model is 'seurat', then returns a list of heatmaps (1 for each batch) that may be subsequently plotted individually

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_lg <- selectFeatures(my_phemdObj_lg, selected_genes)
my_phemdObj_monocle <- embedCells(my_phemdObj_lg, data_model = 'gaussianff',
pseudo_expr=0, sigma=0.02, maxIter=2)
my_phemdObj_monocle <- orderCellsMonocle(my_phemdObj_monocle)
myheatmap <- plotHeatmaps(my_phemdObj_monocle, cell_model='monocle2')

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