plotVolcano | R Documentation |
Construct a volcano plot
plotVolcano(
res,
logFCCol = NULL,
pvalCol = NULL,
padjCol = NULL,
padjThreshold = 0.05,
pointSize = "small",
interactivePlot = FALSE,
nTopToLabel = 0
)
res |
|
logFCCol , pvalCol , padjCol |
Character scalars indicating the
columns from |
padjThreshold |
Numeric scalar indicating the adjusted p-value threshold to use for coloring the points. All features with adjusted p-value below the treshold will be shown in red. |
pointSize |
Either |
interactivePlot |
Logical scalar, indicating whether an interactive plot should be returned, in which one can hover over the individual points and obtain further information. |
nTopToLabel |
Numeric scalar, indicating the number of points that
should be labeled in the plot. The points will be ranked by the
|
If interactivePlot
is TRUE
, a plotly
object. If interactivePlot
is FALSE
, a ggplot2
object.
Charlotte Soneson
se <- readRDS(system.file("extdata", "GSE102901_cis_se.rds",
package = "mutscan"))[1:200, ]
design <- model.matrix(~ Replicate + Condition,
data = SummarizedExperiment::colData(se))
res <- calculateRelativeFC(se, design, coef = "Conditioncis_output")
plotVolcano(res, pointSize = "large", nTopToLabel = 3)
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