easyMAplot: Interactive MA plot labels

In easylabel: Interactive Scatter Plot and Volcano Plot Labels

Interactive MA plot labels

Description

Interactive labelling of MA plots using shiny/plotly interface.

Usage

easyMAplot(
  data,
  x = NULL,
  y = NULL,
  padj = NULL,
  fdrcutoff = 0.05,
  colScheme = c("darkgrey", "blue", "red"),
  hline = 0,
  labelDir = "yellipse",
  xlab = expression("log"[2] ~ " mean expression"),
  ylab = expression("log"[2] ~ " fold change"),
  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 mean expression. For DESeq2 and limma objects this is automatically set.
y	Name of the column containing log fold change. For DESeq2 and limma objects this is automatically set.
padj	Name of the column containing adjusted p values (optional). For DESeq2 and limma objects this is automatically set. If y is specified and padj is left blank or equal to y, nominal unadjusted p values are used for cut-off for significance.
fdrcutoff	Cut-off for FDR significance. Defaults to FDR < 0.05. Can be vector with multiple cut-offs. To use nominal P values instead of adjusted p values, set y but leave padj blank.
colScheme	Colour colScheme. Length must match either length(fdrcutoff) + 1 to allow for non-significant genes, or match length(fdrcutoff) * 2 + 1 to accommodates asymmetric colour colSchemes for positive & negative fold change. (see examples).
hline	Vector of horizontal lines (default is y = 0).
labelDir	Option for label lines. See easylabel().
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() easyVolcano()

easylabel documentation built on May 29, 2024, noon