plotHeatmaps {phemd}R Documentation

Plot heatmap of cell subtypes

Description

Takes as input a Phemd object containing either a Monocle2 or Seurat object (already embedded and ordered) and saves heatmap describing cell subtypes to specified folder

Usage

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

Arguments

obj

'Phemd' object containing Monocle 2 object

cell_model

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

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 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')


[Package phemd version 1.0.0 Index]