spia_plotBubble: Make a bubblePlot for SPIA pathway output

In vivekbhr/vivlib: An R package for useful bioinformatics wrappers

Description

Make a bubblePlot for SPIA pathway output

Usage

spia_plotBubble(SPIAout, outfileName = NULL, top = 20, plotType = 1,
  title = NULL)

Arguments

SPIAout	output from spia_wrapper
outfileName	output pdf file name for plot
top	How many top pathways to plot (by pGFdr value)
plotType	Which kind of bubble plot to make. options are : 1 (activated and inactivated pathways together) or 2 (activated and inactivated pathways split by a horizontal line). Note that in type 2 the p values appear as negative for inactivated pathways.
title	Title of the plot

Value

plot A bubbleplot in pdf format

Examples

## Not run: 
deout <- system.file("extdata", "edgeR_output_annotated.tsv", package="vivlib")
spia_wrapper(DEoutput = deout, organism = "mmu", outFile = "edgeR_spia.txt")
spia_plotBubble(SPIAout = "edgeR_spia.txt", outfileName = "SPIAplots.out", top = 20, title = "SPIA plot")

## End(Not run)

vivekbhr/vivlib documentation built on May 3, 2019, 6:13 p.m.