Visualization of marker expression in a data set or of predefined genes (B cells, CD4 T cells and CD8 T cells).

Visualization of marker expression in a data set or of predefined genes (B cells, CD4 T cells and CD8 T cells).

GEX_gene_visualization(
  GEX,
  gene_set,
  predefined_genes = c("B_cell", "CD4_T_cell", "CD8_T_cell"),
  group.by
)

Arguments

GEX

GEX output of the VDJ_GEX_matrix function (VDJ_GEX_matrix[[2]])).

gene_set

Character vector containing the markers of interest given by the user.

predefined_genes

Character vector to chose between B_cell, CD4_T_cell, and CD8_T_cell.

group.by

Character. Column name of vgm to group plots by

Value

Return a list. Element[[1]] is the feature plot of markers of interest or predefined genes. Element[[2]] is the dottile plot of markers of interest or predefined genes. Element[[3]] is the violin plot of markers of interest or predefined genes.

Examples

if (FALSE) {
# Pre-defined gene set for CD4 T cells
GEX_gene_visualization(GEX = VGM$GEX, predefined_genes = "CD4_T_cell")

# Pre-defined gene set for CD8 T cells
GEX_gene_visualization(GEX = VGM$GEX, predefined_genes = "CD8_T_cell")

# Pre-defined gene set for B cells
GEX_gene_visualization(GEX = VGM$GEX, predefined_genes = "B_cell")

# Gene set defined by user
GEX_gene_visualization(GEX = VGM$GEX, gene_set=c("CD8A","CD3E","SELL","FAS","ID3","SDC1"))
}