cellTypeAssignMarkerGenes {CDSeq}R Documentation

cellTypeAssignMarkerGenes assigns CDSeq-identified cell types using user-provided marker gene list and plots heatmap.

Description

cellTypeAssignMarkerGenes assigns CDSeq-identified cell types using user-provided marker gene list and plots heatmap.

Usage

cellTypeAssignMarkerGenes(
  cell_gep = NULL,
  marker_gene_list = NULL,
  threshold = 2,
  fig_path = getwd(),
  rowlabelsize = 1,
  collabelsize = 1,
  margins = c(3, 0),
  fig_width = 100,
  fig_height = 100,
  keysize = 1,
  srtcol = 45,
  keypar = c(3.5, 0, 3, 0),
  heatmap_name = "cellTypeAssign_heatmap.pdf",
  heatmap_name_fuzzy_assign = "cellTypeAssign_heatmap_fuzzy.pdf",
  verbose = FALSE
)

Arguments

cell_gep

gene expression profile matrix with G rows (genes) and M columns (cell types).

marker_gene_list

a G (genes) by C (cell types with known identities) matrix or dataframe that contains the marker genes for each cell type. Column names must be CellType and GeneName.

threshold

a numeric value that provides the threshold of whether a known cell type in the marker gene list can be identified.

fig_path

the location where the heatmap figure is saved.

rowlabelsize

row label size

collabelsize

column label size

margins

a vector of length 2 indicates row and column label margins

fig_width

figure width for pdf figure

fig_height

figure height for pdf figure

keysize

color key size for heatmap

srtcol

column label angle

keypar

color key layout

heatmap_name

the name of heatmap figure of one-to-one assignment.

heatmap_name_fuzzy_assign

the name of heatmap figure of fuzzy assignment.

verbose

if TRUE, some information will be printed.

Value

cellTypeAssignMarkerGenes returns a list containing: GEP_markerSum (a A by B matrix where A is nrow(marker_gene_list), B is ncol(cell_gep)),

GEP_markerSum_zscore (row-wise z score of GEP_markerSum),

GEP_matched is cell_gep(,cell_type_idx),

cell_type_idx (column index of cell_gep that are considered matching with cell types in marker_gene_list),

cell_type_matched stores the cell types in marker_gene_list that are considered to be matched with cell_gep,

GEP_markerSum_zscore_matched contains only the rows of GEP_markerSum_zscore that are considered to be matched with some cell types in cell_gep. GEP_markerSum_zscore_matched and GEP_markerSum_zscore have same columns.

cell_type_matched_fuzzy is a zero-one matrix that has the same size as GEP_markerSum_zscore_matched. If (i,j) element is one, means ith cell type in marker_gene_list is assigned to jth element in cell_gep.


[Package CDSeq version 1.0.8 Index]