Create an interactive labeled MA plot — plotMA.label

This function creates an MA plot from a data.frame containing DE analysis results using plot_ly

Usage

plotMA.label_ly(
  res,
  fdr.thres = 0.01,
  fc.thres = 0,
  fc.lim = NULL,
  lab.genes = NULL,
  tolower.cols = c("SYMBOL", "ALIAS")
)

Arguments

res: data.frame with DE analysis results. Must contain "padj" & "log2FoldChange" columns
fdr.thres: False discovery rate (FDR) threshold
fc.thres: log2FoldChange threshold
fc.lim: y-axis limits
lab.genes: genes to label on MA plot
tolower.cols: column names that will be converted to lower case

Value

plotly handle

Examples

library(DESeq2)

# make example DESeq dataset
dds <- makeExampleDESeqDataSet()

# run DE analysis
dds <- DESeq(dds)
#> estimating size factors
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing

# extract comparison of interest
res <- results(dds, contrast = c("condition", "A", "B"))

# add gene and symbol column
res$gene <- rownames(res)
res$symbol <- rownames(res)

plotMA.label(res, lab.genes = c("gene1", "gene2"))
#> Warning: log-10 transformation introduced infinite values.