SkeletalVis (version 0.1.2)

volcano_plot: Volcano Plot of Gene Expression Data

Description

Creates a volcano plot showing the log2 fold change and FDR values with optional labelling of points.

Usage

volcano_plot(
  data,
  number_points = 5,
  selected_points = NULL,
  interactive = FALSE,
  logFC_threshold = log2(1.5),
  FDR_threshold = 0.05,
  point_size = 2,
  lab_size = 4
)

Value

A ggplot object representing the volcano plot.

Arguments

data

A data frame containing gene expression data, containing an ID, log2 foldchange and FDR columns.

number_points

Number of top up and down regulated points to label

selected_points

Character vector of the IDs to label

interactive

Should an interactive plotly graph be made?

logFC_threshold

The foldchange threshold to define up and down regulated points

FDR_threshold

The pval threshold to define up and down regulated points

point_size

Size for the points

lab_size

Size for the labels

Examples

skeletalvis <- load_skeletalvis(demo=TRUE)

experiment_results <- get_experiment(skeletalvis, "GSE155118_1")

volcano_plot(experiment_results)