plotHicRectangle {plotgardener} | 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.
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.
## 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()