Platypus (version 3.6.0)

GEX_volcano: 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
)

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.

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.

Examples

# \donttest{
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)
})
# }