View source: R/plotHicRectangle.R
plotHicRectangle | R Documentation |
Plot a triangular Hi-C interaction matrix in a rectangular format
plotHicRectangle(
data,
resolution = "auto",
zrange = NULL,
norm = "KR",
matrix = "observed",
chrom,
chromstart = NULL,
chromend = NULL,
assembly = "hg38",
palette = colorRampPalette(brewer.pal(n = 9, "YlGnBu")),
colorTrans = "linear",
flip = FALSE,
bg = NA,
x = NULL,
y = NULL,
width = NULL,
height = NULL,
just = c("left", "top"),
default.units = "inches",
draw = TRUE,
params = NULL,
quiet = FALSE
)
data |
Path to .hic file as a string or a 3-column dataframe of interaction counts in sparse upper triangular format. |
resolution |
A numeric specifying the width in basepairs of each pixel. For hic files, "auto" will attempt to choose a resolution based on the size of the region. For dataframes, "auto" will attempt to detect the resolution the dataframe contains. |
zrange |
A numeric vector of length 2 specifying the range of interaction scores to plot, where extreme values will be set to the max or min. |
norm |
Character value specifying hic data normalization method,
if giving .hic file. This value must be found in the .hic file.
Default value is |
matrix |
Character value indicating the type of matrix to output.
Default value is
|
chrom |
Chromosome of region to be plotted, as a string. |
chromstart |
Integer start position on chromosome to be plotted. |
chromend |
Integer end position on chromosome to be plotted. |
assembly |
Default genome assembly as a string or a
assembly object.
Default value is |
palette |
A function describing the color palette to use for
representing scale of interaction scores. Default value is
|
colorTrans |
A string specifying how to scale Hi-C colors.
Options are "linear", "log", "log2", or "log10".
Default value is |
flip |
A logical indicating whether to flip the orientation of
the Hi-C matrix over the x-axis. Default value is |
bg |
Character value indicating background color.
Default value is |
x |
A numeric or unit object specifying rectangle Hi-C plot x-location. |
y |
A numeric, unit object, or character containing a "b" combined with a numeric value specifying rectangle Hi-C plot y-location. The character value will place the rectangle Hi-C plot y relative to the bottom of the most recently plotted plot according to the units of the plotgardener page. |
width |
A numeric or unit object specifying the width of the Hi-C plot rectangle. |
height |
A numeric or unit object specifying the height of the Hi-C plot rectangle. |
just |
Justification of rectangle Hi-C plot relative to
its (x, y) location. If there are two values, the first value
specifies horizontal justification and the second value specifies
vertical justification.
Possible string values are: |
default.units |
A string indicating the default units to use
if |
draw |
A logical value indicating whether graphics output should
be produced. Default value is |
params |
An optional pgParams object containing relevant function parameters. |
quiet |
A logical indicating whether or not to print messages. |
This function is similar is plotHicTriangle but will fill in additional pixels around the the triangular portion of the plot to make a rectangle. The x-axis represents the genomic coordinates and the y-axis corresponds to distance in Hi-C bins.
A rectangle Hi-C plot can be placed on a plotgardener coordinate page by providing plot placement parameters:
plotHicRectangle(data, chrom, chromstart = NULL, chromend = NULL, x, y, width, height, just = c("left", "top"), default.units = "inches")
This function can also be used to quickly plot an unannotated rectangle Hi-C plot by ignoring plot placement parameters:
plotHicRectangle(data, chrom, chromstart = NULL, chromend = NULL)
Returns a hicRectangle
object containing
relevant genomic region, Hi-C data, placement,
and grob information.
readHic, plotHicTriangle
## Load Hi-C data
library(plotgardenerData)
data("IMR90_HiC_10kb")
## Create a page
pageCreate(width = 6, height = 3.5, default.units = "inches")
## Plot and place rectangle Hi-C plot
hicPlot <- plotHicRectangle(
data = IMR90_HiC_10kb, resolution = 10000,
zrange = c(0, 70),
chrom = "chr21",
chromstart = 28950000, chromend = 29800000,
assembly = "hg19",
x = 0.5, y = 0.5, width = 5, height = 2.5,
just = c("left", "top"),
default.units = "inches"
)
## Annotate x-axis genome label
annoGenomeLabel(
plot = hicPlot, scale = "Kb", x = 0.5, y = 3.03,
just = c("left", "top")
)
## Annotate heatmap legend
annoHeatmapLegend(
plot = hicPlot, x = 5.6, y = 0.5,
width = 0.13, height = 1.5,
just = c("left", "top")
)
## Hide page guides
pageGuideHide()
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