Plot assay values stratified by sequence context

Usage

plotValsBySeqContext(
  se,
  seqContextColumn = "sequenceContext",
  assayName = "mod_prob",
  aggregation = "mean",
  selectContextsBy = "sample_union",
  facetBy = NULL,
  fillBy = NULL,
  fillColors = "grey",
  plotType = "violin",
  topN = 10,
  bottomN = 10,
  flipCoord = TRUE,
  yAxisLabel = "Modification probability"
)

Arguments

se: SummarizedExperiment object with read-level footprinting data. Rows should correspond to positions and columns to samples.
seqContextColumn: Character scalar indicating which column of rowData(se) contains the sequence context.
assayName: Character scalar indicating from which read-level assay the values to plot should be extracted.
aggregation: Character scalar indicating if/how to aggregate values across (samples and) reads before plotting. Must be one of "none" (no aggregation, individual values from the assay are plotted) and "mean" (calculate average value for each position before plotting).
selectContextsBy: Character scalar indicating how to select and order the contexts to show in the plot. Should be one of "sample" (in which case the selection of sequence contexts will be done independently for each sample, and only the ones selected for a given sample will be displayed in the plot panel for that sample; in this case facetBy must be "sample"), "sample_union" ( in which case the selection of sequence contexts will be done for each sample, and the union of all selected contexts will be shown in the plot), "overall" (in which case the selection of sequence contexts will be made without considering the sample information) or "sample_var" (in which case the variance across samples will be used to select/order contexts). Note that for "sample_union", the plots may contain more than topN + bottomN contexts. For "sample_union" and "overall", the order of the contexts in the plots will be determined by the average value across samples).
facetBy: Character scalar indicating how to facet values in the plot. Must be either NULL (in which case no facetting is done, and values are aggregated across all samples in se) or "sample" (in which case values are aggregated within each sample, and plots are facetted accordingly). Ignored if plotType = "pairs".
fillBy: Character scalar indicating how to fill the bars or violins. Must be either NULL (in which case a single value should be specified to "fillColors" and used for all bars/violins) or "sample" (in which case bars or violins will be split and filled by sample). Ignored if plotType = "pairs".
fillColors: Either a (preferably named) character vector defining the color to use for each sample if fillBy = "sample", or a single color to use for all violins/bars.
plotType: Character scalar indicating what type of plot to create. Should be one of "violin" (note that the violins will be plotted with scale="width"), "bar", "errorbar" or "pairs".
topN, bottomN: Numeric scalars determining the number of sequence contexts to include in the plot. The topN contexts with the highest average values and the bottomN contexts with the lowest average values will be displayed. If facetBy = "sample", the selection of contexts to show is performed separately within each sample.
flipCoord: Logical scalar indicating whether the plot axes should be flipped (to display sequence contexts on the y-axis and values on the x-axis) or not.
yAxisLabel: Character scalar providing the label to display on the value axis.

Value

A ggplot object.

Author

Charlotte Soneson

Examples

modbamfile <- system.file("extdata", c("6mA_1_10reads.bam", "6mA_2_10reads.bam"),
                          package = "footprintR")
ref <- Biostrings::readDNAStringSet(system.file("extdata", "reference.fa.gz",
                                                package = "footprintR"))
se <- readModBam(bamfiles = modbamfile, regions = "chr1", modbase = "a",
                 BPPARAM = BiocParallel::SerialParam())
se <- addSeqContext(se, sequenceContextWidth = 3, sequenceReference = ref)
se <- filterPositions(se, filters = "sequenceContext", sequenceContext = "NAN")
plotValsBySeqContext(se, assayName = "mod_prob", plotType = "violin",
                     topN = 3, bottomN = 3)

plotValsBySeqContext(se, assayName = "mod_prob", plotType = "bar",
                     topN = 3, bottomN = 3)

plotValsBySeqContext(se, assayName = "mod_prob", plotType = "bar",
                     topN = 3, bottomN = 3, facetBy = "sample")