View source: R/GEX_gene_visualization.R
GEX_gene_visualization | R Documentation |
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 )
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 |
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.
## Not run: # 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")) ## End(Not run)
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