Interactive labelling of MA plots using shiny/plotly interface.
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,
...
)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 mean expression. For DESeq2 and limma objects this is automatically set.
Name of the column containing log fold change. For DESeq2 and limma objects this is automatically set.
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.
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.
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).
Vector of horizontal lines (default is y = 0).
Option for label lines. See easylabel().
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() easyVolcano()