interactiveMAplot: Interactive version of plotMA from the limma package.
In Shians/Glimma-deprecated: Interactive graphics from the limma package

Description Usage Arguments Details Value Author(s) References See Also Examples

This function produces a MA plot that the user can search for genes, plot counts per million and SA plot.

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interactiveMAplot(object, y, p.value=0.05, lfc=0, adjust.method="BH", groups, labels=NULL, coef=NULL,
                  searchBy="Symbols", dir=NULL, launch=TRUE, main=NULL, url=NULL, urlGeneIDs=NULL, displayGeneIDs="Symbols")

`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).
`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).
`searchBy`	character string specifying gene annotation column to allow searching by in final plot.
`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.
`url`	character string specifying URL to use to link out to external gene ID information.
`urlGeneIDs`	character string specifying the gene annotation column to use as key at specified `url`.
`displayGeneIDs`	character string (or vector) specifying the gene annotation column/(s) to display in plot.

This function generates an interactive MA plot.

A html page with a searchable MA plot, with a second panel displyaing 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.

Shian Su, Matt Ritchie

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.

interactivebarcodeplot

## 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
  plotMDS(x, labels=1:7, col=as.numeric(genotype), main="MDS plot for Smchd1 experiment")
  legend("topright", legend=c("WT", "Smchd1 null"), pch=15, col=1:2)

  # 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)
  interactiveMAplot(vfit, v, groups=genotype, coef=2)

## End(Not run)