PlotPSEAIntegPaths: PlotPSEAIntegPaths

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

PlotPSEAIntegPaths

Description

Plots both the original mummichog and the GSEA results by combining p-values using the Fisher's method (sumlog).

Usage

PlotPSEAIntegPaths(
  mSetObj = NA,
  imgName = "",
  format = "png",
  dpi = 72,
  width = 9,
  labels = "default",
  labels.x = 5,
  labels.y = 5,
  scale.axis = TRUE,
  interactive = F
)

Arguments

mSetObj	Input the name of the created mSetObj object
imgName	Input a name for the plot
format	Character, input the format of the image to create.
dpi	Numeric, input the dpi of the image to create.
width	Numeric, input the width of the image to create.
labels	Character, indicate if the plot should be labeled. By default it is set to "default", and the 5 top-ranked pathways per each algorithm will be plotted. Users can adjust the number of pathways to be annotated per pathway using the "labels.x" and "labels.y" parameters. Users can set this to "none" for no annotations, or "all" to annotate all pathways.
labels.x	Numeric, indicate the number of top-ranked pathways using the fGSEA algorithm to annotate on the plot.
labels.y	Numeric, indicate the number of top-ranked pathways using the original mummichog algorithm to annotate on the plot.
scale.axis	logical, TRUE to scale

Author(s)

Jasmine Chong, Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR documentation built on Dec. 23, 2024, 3:44 p.m.