easyVolcano: Interactive volcano plot labels

View source: R/easyVolcano.R

easyVolcanoR Documentation

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 Oct. 25, 2023, 1:07 a.m.