easyMAplot {easylabel}

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()