Interactive labelling of volcano plots using shiny/plotly interface.
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,
...
)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().
The dataset for the plot. Automatically attempts to recognises DESeq2 and limma objects.
Name of the column containing log fold change. For DESeq2 and limma objects this is automatically set.
Name of the column containing p values. For DESeq2 and limma objects this is automatically set.
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.
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.
Optional vector of log fold change cut-offs.
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).
x axis title. Accepts expressions.
y axis title. Accepts expressions.
Filename for saving to pdf.
Logical whether to show legend with number of differentially expressed genes.
Logical whether to convert nominal P values to q values. Requires the qvalue Bioconductor package.
Other arguments passed to easylabel().
easylabel() easyMAplot()