GEX_gene_visualization: Visualization of marker expression in a data set or of...

In Platypus: Single-Cell Immune Repertoire and Gene Expression Analysis

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
)

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

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

Platypus documentation built on Oct. 18, 2024, 5:08 p.m.