Plot single-molecule footprinting data for a single genomic region.

This function will visualize read-level or collapsed single-molecule footprinting data, such as data imported using readModkitExtract or readBedMethyl.

Usage

plotRegion(
  se,
  region = NULL,
  tracks = list(list(trackData = "FracMod", trackType = "Point")),
  modbaseSpace = FALSE,
  sequenceContext = NULL
)

Arguments

se

A SummarizedExperiment object with read-level or collapsed single-molecule footprinting data (positions in rows and reads or samples in columns).

region

A GRanges object with a single region. Only data from se overlapping this region will be plotted. Alternatively, the region can be specified as a character scalar (e.g. "chr1:1200-1300") that can be coerced into a GRanges object. If NULL (the default), all the data on the first sequence in se will be visualized.

tracks

A list of named lists, representing the tracks to generate. Each element of the outer list defines one track, and has to contain at least list entries named 'trackData' (the name of a suitable assay in se) and 'trackType' (the type of plot), plus any additional arguments to the respective plot function. Currently supported plot types are

"Point"

: A point plot displaying values in the assay.

"Smooth"

: A smoothed line plot displaying values in the assay.

"PointSmooth"

: A point and smoothed line plot displaying values in the assay.

"Lollipop"

: Lollipop plot (filled circles with the color representing the values in the assay).

"Heatmap"

: Heatmap plot (tiles with the color representing the values in the assay).

modbaseSpace

A logical scalar. If TRUE, the x-axis will be shown in the space of modified bases and contain only the positions at which there are modified bases in the data without any gaps between them. If FALSE, the x-axis will show the genomic coordinate on which the modified bases are typically irregularly spaced.

sequenceContext

A character vector with sequence context(s) to plot. Only positions that match one of the provided sequence contexts will be included in the plot. Sequence contexts can be provided using IUPAC redundancy codes. The sequence contexts of modified bases are obtained from rowData(se)$sequenceContext and thus requires that se contains the appropriate information, for example by setting the sequenceContext and sequenceReference arguments of readBedMethyl when it was generated, or by adding it using addSeqContext.

Value

A ggplot object with tracks selected by tracks.

See also

readModBam, readModkitExtract and readBedMethyl for reading read-level and summarized footprinting data.

Author

Charlotte Soneson, Michael Stadler

Examples

# summarized data (5mC)
bmfiles <- system.file("extdata",
                       c("modkit_pileup_1.bed.gz", "modkit_pileup_2.bed.gz"),
                       package = "footprintR")
reffile <- system.file("extdata", "reference.fa.gz", package = "footprintR")

seA <- readBedMethyl(bmfiles, modbase = "m",
                     sequenceContextWidth = 3, sequenceReference = reffile)

plotRegion(seA, region = "chr1:6940000-6955000", sequenceContext = "GCH")

plotRegion(seA, region = "chr1:6940000-6955000", sequenceContext = "HCG")


plotRegion(seA, region = "chr1:6940000-6955000",
           tracks = list(list(trackData = "Nvalid", trackType = "Smooth")))


# read-level data (6mA)
extractfiles <- system.file("extdata",
                            c("modkit_extract_rc_6mA_1.tsv.gz",
                              "modkit_extract_rc_6mA_2.tsv.gz"),
                            package = "footprintR")
seB <- readModkitExtract(extractfiles, modbase = "a", filter = "modkit")

# Lollipop plot
plotRegion(seB, region = "chr1:6935800-6935900",
           tracks = list(list(trackData = "mod_prob", trackType = "Lollipop")))
#> Warning: the standard deviation is zero

# Heatmap plots (observed only or filled)
plotRegion(seB, region = "chr1:6935800-6935900",
           tracks = list(list(trackData = "mod_prob", trackType = "Heatmap")))
#> Warning: the standard deviation is zero

plotRegion(seB, region = "chr1:6935800-6935900",
           tracks = list(list(trackData = "mod_prob", trackType = "Heatmap",
                              interpolate = TRUE)))
#> Warning: the standard deviation is zero


# multiple plots
plotRegion(seB, region = "chr1:6935400-6935450",
           tracks = list(list(trackData = "mod_prob", trackType = "Lollipop",
                              size = 4),
                         list(trackData = "mod_prob", trackType = "Heatmap")),
           modbaseSpace = TRUE)