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@@ -3,7 +3,7 @@ |
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#' Plotting functions for enrichment analysis of \code{\link{multiHMM}} or \code{\link{combinedMultiHMM}} objects with any annotation of interest, specified as a \code{\link[GenomicRanges]{GRanges-class}} object.
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| 4 | 4 |
#' |
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#' @name enrichment_analysis |
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-#' @param combinations A vector with combinations for which the enrichment will be calculated. If \code{NULL} all combinations will be considered.
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+#' @param combinations A vector with combinations for which the enrichment will be calculated, e.g. \code{combinations = c('[H3K4me3]','[H3K4me3+H3K27me3]')}. If \code{NULL} all combinations will be considered.
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#' @param marks A vector with marks for which the enrichment is plotted. If \code{NULL} all marks will be considered.
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#' @param logscale Set to \code{TRUE} to plot fold enrichment on log-scale. Ignored if \code{statistic = 'fraction'}.
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#' @return A \code{\link[ggplot2:ggplot]{ggplot}} object containing the plot or a list() with \code{\link[ggplot2:ggplot]{ggplot}} objects if several plots are returned. For \code{plotFoldEnrichHeatmap} a named array with fold enrichments if \code{plot=FALSE}.
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| ... | ... |
@@ -48,7 +48,7 @@ plotEnrichment( |
| 48 | 48 |
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| 49 | 49 |
\item{what}{One of \code{c('combinations','peaks','counts','transitions')} specifying on which feature the statistic is calculated.}
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| 50 | 50 |
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| 51 |
-\item{combinations}{A vector with combinations for which the enrichment will be calculated. If \code{NULL} all combinations will be considered.}
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+\item{combinations}{A vector with combinations for which the enrichment will be calculated, e.g. \code{combinations = c('[H3K4me3]','[H3K4me3+H3K27me3]')}. If \code{NULL} all combinations will be considered.}
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| 52 | 52 |
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| 53 | 53 |
\item{marks}{A vector with marks for which the enrichment is plotted. If \code{NULL} all marks will be considered.}
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| 54 | 54 |
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