Flexible wrapper for GEX volcano plots — GEX

Plots a volcano plot from the output of the FindMarkers function from the Seurat package or the GEX_cluster_genes function alternatively.

GEX_volcano(
  DEGs.input,
  input.type,
  condition.1,
  condition.2,
  explicit.title,
  RP.MT.filter,
  color.p.threshold,
  color.log.threshold,
  label.p.threshold,
  label.logfc.threshold,
  n.label.up,
  n.label.down,
  by.logFC,
  maximum.overlaps,
  plot.adj.pvalue
)

Arguments

DEGs.input: Either output data frame from the FindMarkers function from the Seurat package or GEX_cluster_genes list output.
input.type: Character specifing the input type as either "findmarkers" or "cluster.genes". Defaults to "cluster.genes"
condition.1: either character or integer specifying ident.1 that was used in the FindMarkers function from the Seurat package. Should be left empty when using the GEX_cluster_genes output.
condition.2: either character or integer specifying ident.2 that was used in the FindMarkers function from the Seurat package. Should be left empty when using the GEX_cluster_genes output.
explicit.title: logical specifying whether the title should include logFC information for each condition.
RP.MT.filter: Boolean. Defaults to TRUE. Whether to exclude ribosomal and mitochondrial genes.
color.p.threshold: numeric specifying the adjusted p-value threshold for geom_points to be colored. Default is set to 0.01.
color.log.threshold: numeric specifying the absolute logFC threshold for geom_points to be colored. Default is set to 0.25.
label.p.threshold: numeric specifying the adjusted p-value threshold for genes to be labeled via geom_text_repel. Default is set to 0.001.
label.logfc.threshold: numeric specifying the absolute logFC threshold for genes to be labeled via geom_text_repel. Default is set to 0.75.
n.label.up: numeric specifying the number of top upregulated genes to be labeled via geom_text_repel. Genes will be ordered by adjusted p-value. Overrides the "label.p.threshold" and "label.logfc.threshold" parameters.
n.label.down: numeric specifying the number of top downregulated genes to be labeled via geom_text_repel. Genes will be ordered by adjusted p-value. Overrides the "label.p.threshold" and "label.logfc.threshold" parameters.
by.logFC: logical. If set to TRUE n.label.up and n.label.down will label genes ordered by logFC instead of adjusted p-value.
maximum.overlaps: integer specifying removal of labels with too many overlaps. Default is set to Inf.
plot.adj.pvalue: logical specifying whether adjusted p-value should by plotted on the y-axis.

Value

Returns a volcano plot from the output of the FindMarkers function from the Seurat package, which is a ggplot object that can be modified or plotted. Infinite p-values are set defined value of the highest -log(p) + 100.

Examples

if (FALSE) {
#using the findmarkers.output
GEX_volcano(findmarkers.output = FindMarkers.Output
, condition.1 = "cluster1", condition.2 = "cluster2"
, maximum.overlaps = 20)

GEX_volcano(findmarkers.output = FindMarkers.Output
, condition.1 = "cluster1", condition.2 = "cluster2"
, n.label.up = 50, n.label.down = 20)

#using the GEX_cluster_genes output
GEX_volcano(findmarkers.output = GEX_cluster_genes.Output
, cluster.genes.output =TRUE)
}