GEX_volcano | R Documentation |
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 )
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. |
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.
## Not run: #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) ## End(Not run)
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