GEX_volcano: Flexible wrapper for GEX volcano plots

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

Flexible wrapper for GEX volcano plots

Description

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

Usage

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

try({
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)

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

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