cellTypeAssignMarkerGenes assigns CDSeq-identified cell types using user-provided marker gene list and plots heatmap.cellTypeAssignMarkerGenes assigns CDSeq-identified cell types using user-provided marker gene list and plots heatmap.
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
)gene expression profile matrix with G rows (genes) and M columns (cell types).
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.
a numeric value that provides the threshold of whether a known cell type in the marker gene list can be identified.
the location where the heatmap figure is saved.
row label size
column label size
a vector of length 2 indicates row and column label margins
figure width for pdf figure
figure height for pdf figure
color key size for heatmap
column label angle
color key layout
the name of heatmap figure of one-to-one assignment.
the name of heatmap figure of fuzzy assignment.
if TRUE, some information will be printed.
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.