volcano_plot {SkeletalVis} | R Documentation |
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
)
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 |
Value
A ggplot object representing the volcano plot.
Examples
skeletalvis <- load_skeletalvis(demo=TRUE)
experiment_results <- get_experiment(skeletalvis, "GSE155118_1")
volcano_plot(experiment_results)
[Package SkeletalVis version 0.1.1 Index]