Platypus (version 3.6.0)

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

Description

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

Usage

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

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

Examples

GEX_gene_visualization(GEX = Platypus::small_vgm[[2]], predefined_genes = "B_cell")