gsea_plotly: Interactive Gene Set Enrichment Analysis Plot

In stephenslab/pathways: Gene Set Enrichment Analysis Using Human and Mouse Gene Sets

Description

Create an interactive scatterplot to explore the results of a gene set enrichment analysis. In the plot, one point is drawn for each gene set. The color and shape of the points are varied the gene set database. To compare results across multiple analyses, the p-value for the selected analysis (or column) is plotted on the vertical axis, and the “most extreme” p-value from the other analyses (or columns) is plotted along the horizontal axis.

Usage

gsea_plotly(
  gsea_res,
  gene_set_info,
  k,
  file,
  height = 600,
  width = 800,
  title = "gsea plot",
  max_name_len = 44,
  colors = c("gold", "darkblue", "tomato", "dodgerblue", "darkmagenta", "yellowgreen",
    "dodgerblue", "olivedrab", "firebrick", "darkorange", "magenta", "darkblue", "gold",
    "tomato", "gold", "olivedrab", "darkblue", "darkorange", "magenta", "yellowgreen",
    "tomato", "dodgerblue"),
  shapes = c(rep("circle", 4), rep("x", 10), rep("diamond", 8))
)

Arguments

gsea_res	An output from perform_gsea.
gene_set_info	A data frame containing information about the gene sets. It should have, at a minimum, columns “name”, “id” and “database”.
k	The column of the gene set enrichment results used for the plot.
file	Save the interactive plot to this HTML file using saveWidget.
height	Height of the plot in pixels. Passed as argument “height” to plot_ly.
width	Width of the plot in pixels. Passed as argument “width” to plot_ly.
title	The text used for the plot title.
max_name_len	Pathway names longer than this are shortened to this number of characters.
colors	Colors used to draw the points in the plot; passed as argument “colors” to plot_ly.
shapes	Shapes used to draw the points in the plot; passed as argument “shapes” to plot_ly.

Value

A plotly object.

See Also

perform_gsea

Examples

# See perform_gsea for examples.

stephenslab/pathways documentation built on March 17, 2021, 11:03 p.m.