easyVolcano: Interactive volcano plot labels

In easylabel: Interactive Scatter Plot and Volcano Plot Labels

Interactive volcano plot labels

Description

Interactive labelling of volcano plots using shiny/plotly interface.

Usage

easyVolcano(
  data,
  x = NULL,
  y = NULL,
  padj = y,
  fdrcutoff = 0.05,
  fccut = NULL,
  colScheme = c("darkgrey", "blue", "red"),
  xlab = expression("log"[2] ~ " fold change"),
  ylab = expression("-log"[10] ~ " P"),
  filename = NULL,
  showCounts = TRUE,
  useQ = FALSE,
  ...
)

Arguments

data	The dataset for the plot. Automatically attempts to recognises DESeq2 and limma objects.
x	Name of the column containing log fold change. For DESeq2 and limma objects this is automatically set.
y	Name of the column containing p values. For DESeq2 and limma objects this is automatically set.
padj	Name of the column containing adjusted p values (optional). If y is specified and padj is left blank or equal to y, nominal unadjusted p values are used for cut-off for significance instead of adjusted p values.
fdrcutoff	Cut-off for FDR significance. Defaults to FDR < 0.05. If y is specified manually and padj is left blank then this refers to the cut-off for significant points using nominal unadjusted p values.
fccut	Optional vector of log fold change cut-offs.
colScheme	Colour scheme. If no fold change cut-off is set, 2 colours need to be specified. With a single fold change cut-off, 3 or 5 colours are required, depending on whether the colours are symmetrical about x = 0. Accommodates asymmetric colour schemes with multiple fold change cut-offs (see examples).
xlab	x axis title. Accepts expressions.
ylab	y axis title. Accepts expressions.
filename	Filename for saving to pdf.
showCounts	Logical whether to show legend with number of differentially expressed genes.
useQ	Logical whether to convert nominal P values to q values. Requires the qvalue Bioconductor package.
...	Other arguments passed to easylabel().

Value

By default no return value. If output_shiny = FALSE or the shiny button 'Export plotly & exit' is pressed, a plotly figure is returned. See easylabel().

See Also

easylabel() easyMAplot()

easylabel documentation built on May 29, 2024, noon