interactiveMDplot: Interactive version of plotMD from the limma package.

In Shians/Glimma-deprecated: Interactive graphics from the limma package

Description

This function produces a MD (mean-difference) plot that the user can search for genes in, with a second panel showing either the individual expression values or the trend of variability versus abundance (SA plot).

Usage

interactiveMDplot(object, y, groups, genes=NULL, p.value=0.05, lfc=0, adjust.method="BH", labels=NULL, coef=NULL,
                         baseURL="http://www.ncbi.nlm.nih.gov/gene/?term=", searchBy="Symbol", linkBy="GeneID", 
                         dir=NULL, launch=TRUE, main=NULL)

Arguments

object	MArrayLM object output from lmFit or contrasts.fit containing logFCs (M-values) and average expression values (A-values) to be plotted.
y	a RGList, MAList, EList or ExpressionSet containing pre-processed data (both expression and annotation) before linear model has been fitted, used to plot individual expression values in a second panel.
groups	character vector or factor specifying the experimental groups (used to separate expression values for plotting).
genes	data.frame of gene annotation information
p.value	numeric value between 0 and 1 giving the desired size of the test.
lfc	minimum log2-fold-change required to highlight points.
adjust.method	method used to adjust the p-values for multiple testing. Options, in increasing conservatism, include "none", "BH", "BY" and "holm". See p.adjust for details.
labels	character vector specifying sample labels.
coef	numeric scalar indicating which coefficient from the linear model to make an MA plot of (defaults to first coefficient).
baseURL	character string specifying URL to use to link out to external gene ID information.
searchBy	character string specifying column from gene annotation data.frame to allow searching by in plot.
linkBy	character string specifying the column name from the gene annotation data.frame to use as key at specified baseURL.
dir	character string indicating the output directory for the plot.
launch	logical. Should the resulting plot be displayed?
main	character string specifying the title of the html page.

Details

This function generates an interactive MD plot.

Value

A html page with a searchable MD plot, with a second panel displaying either the expression values for a selected gene or an SA plot summarising variability as a function of abundance with the particular gene of interest highlighted. A searchable table of results for the top genes ranked genes is also displayed below the 2 plot panels.

Author(s)

Shian Su, Matt Ritchie

References

Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Research 43, doi: 10.1093/nar/gkv007.

See Also

interactiveMDSplot

Examples

## Not run: 
  library(Glimma)
  library(edgeR)
  load("x.rda")
  # RNA-seq data set available from GEO under accession number GSE64099
  # filter out genes with low read counts
  sel = rowSums(cpm(x$counts)>0.5)>=3
  x = x[sel,]
  x$genes = x$genes[,c(1,3)]
  des = model.matrix(~x$samples$group)
  colnames(des)[2] = "Smchd1nullvsWt"
  x = calcNormFactors(x, method="TMM")
  genotype = x$samples$group

  # See how replicate sample cluster
  interactiveMDSplot(x, labels=1:7, col=as.numeric(genotype), main="MDS plot for Smchd1 experiment")

  # Apply voom with sample quality weights
  v = voomWithQualityWeights(x, design=des, normalization="none", plot=TRUE)
  vfit = lmFit(v)
  vfit = eBayes(vfit)
  topTable(vfit,coef=2,sort.by="P")

  # Make interactive MA plot of results for coefficient of interest (Smchd1 null vs Wt)
  interactiveMDplot(vfit, v, groups=genotype, coef=2, main="Smchd1 null vs Wt")

## End(Not run)

Shians/Glimma-deprecated documentation built on May 9, 2019, 1:26 p.m.