plot_volcano: Volcano plot for log fold changes and log p-values

Description Usage Arguments Details Value Examples

View source: R/plot_volcano.R

Description

Volcano plot for log fold changes and log p-values in the ggplot2 framework, with additional support to annotate genes if provided.

Usage

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plot_volcano(res_obj, FDR = 0.05, ylim_up = NULL, vlines = NULL,
  title = NULL, intgenes = NULL, intgenes_color = "steelblue",
  labels_intgenes = TRUE)

Arguments

res_obj

A DESeqResults object

FDR

Numeric value, the significance level for thresholding adjusted p-values

ylim_up

Numeric value, Y axis upper limits to restrict the view

vlines

The x coordinate (in absolute value) where to draw vertical lines, optional

title

A title for the plot, optional

intgenes

Vector of genes of interest. Gene symbols if a symbol column is provided in res_obj, or else the identifiers specified in the row names

intgenes_color

The color to use to mark the genes on the main plot.

labels_intgenes

Logical, whether to add the gene identifiers/names close to the marked plots

Details

The genes of interest are to be provided as gene symbols if a symbol column is provided in res_obj, or else b< using the identifiers specified in the row names

Value

An object created by ggplot

Examples

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library(airway)
data(airway)
airway
dds_airway <- DESeq2::DESeqDataSetFromMatrix(assay(airway),
                                             colData = colData(airway),
                                             design=~cell+dex)
dds_airway <- DESeq2::DESeq(dds_airway)
res_airway <- DESeq2::results(dds_airway)

plot_volcano(res_airway)

federicomarini/ideal documentation built on Nov. 4, 2018, 10:03 a.m.