plotVolcano: plotVolcano

In IMB-Computational-Genomics-Lab/ascend: ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Description

Produces a volcano plot featuring differential expression results.

Usage

plotVolcano(x, threshold = 0.005, l2fc = 2, labels = FALSE,
  label.size = 5, check.overlap = TRUE)

Arguments

x	Differential expression results generated by runDESeq.
threshold	Threshold to determine significant results by (Default: 5e-3).
l2fc	Threshold to determine significant Log2FoldChange by (Default: 2).
labels	Display names of significant results on plot (Default: FALSE).
label.size	Size of label text (Default: 5).
check.overlap	If labels = TRUE, remove overlapping labels

Value

A scatter plot rendered by ggplot2's geom_point.

Examples

# Load EMSet that has undergone analysis
em_set <- ascend::analyzed_set

# Run differential expression analysis using combined LRT
de_result_df <- runDiffExpression(em_set, group = "cluster", 
condition.a = 1, condition.b = 2, ngenes = 1500, subsampling = FALSE)

# Use function to generate volcano plot
my_volcano_plot <- plotVolcano(de_result_df, threshold = 5e-3, l2fc = 2,
labels = FALSE, check.overlap = FALSE)

IMB-Computational-Genomics-Lab/ascend documentation built on Aug. 29, 2019, 4:10 a.m.