Author: Zuguang Gu ( z.gu@dkfz.de )
Date: 2018-10-30
Package version: 1.12.0
Hilbert curve is a type of space-filling curves that folds one dimensional axis into a two dimensional space, but still keeps the locality. It has advantages to visualize data with long axis in following two aspects:
This package aims to provide an easy and flexible way to visualize data through Hilbert curve. The implementation and example figures are based on following sources:
We first load the packages and set seed for random numbers.
library(HilbertCurve)
library(circlize)
set.seed(12345)
Following shows Hilbert curves with level 2, 3, 4, 5:
As shown in the above plots, as level increases, the length of the curve becomes longer and the curve folds
more densely. The number of segments (one segment is marked in red) on the Hilbert curve is 4^level - 1. If a Hilbert curve with level 11
is used to map to human chromosome 1, the resolution would be 249250621/4^11 (approximately 59bp).
Hilbert curve folds one-dimensional axis into a two-dimensional space while still preserves the locality of the data points. We visualize this attribute with a Hilbert curve with level 5. In following animation, the point moves with its natural order on the axis.
for(i in 1:1024) {
hc = HilbertCurve(1, 1024, level = 5, reference = TRUE, arrow = FALSE)
hc_points(hc, x1 = i, np = NULL, pch = 16, size = unit(2, "mm"))
}
Next, we calculate the pairwise distance between data points in the 2D space and visualize it as heatmap. The numbers on x-axis (top) and y-axis (left) illustrate the position of data points in the original 1D axis.
library(HilbertVis)
pos = HilbertVis::hilbertCurve(5)
mat = as.matrix(dist(pos))
library(ComplexHeatmap)
ht = Heatmap(mat, name = "dist", cluster_rows = FALSE, cluster_columns = FALSE,
show_row_names = FALSE, show_column_names = FALSE,
heatmap_legend_param = list(title = "euclidean_dist"))
draw(ht, padding = unit(c(5, 5, 5, 2), "mm"))
decorate_heatmap_body("dist", {
grid.segments(c(0.25, 0.5, 0.75, 0, 0, 0), c(0, 0, 0, 0.25, 0.5, 0.75),
c(0.25, 0.5, 0.75, 1, 1, 1), c(1, 1, 1, 0.25, 0.5, 0.75), gp = gpar(lty = 2))
grid.text(rev(c(256, 512, 768, 1024)), 0, c(0, 256, 512, 768)/1024, just = "bottom",
rot = 90, gp = gpar(fontsize = 10))
grid.text(c(1, 256, 512, 768, 1024), c(1, 256, 512, 768, 1024)/1024, 1, just = "bottom",
gp = gpar(fontsize = 10))
})
Basically, from the heatmap, data points which are close in the 1D axis are still close in the 2D space (illustrated in the areas around diagonals).
Also there are some data points in (e.g, 1 ~ 256) which are close to data points in (768 ~ 1024)(bottom left or top right area in the heatmap), but it is only due to that the curve folds back. This exception can be easily distinguished by adding assistant grid lines or if users are clear with the structure of the curve.
The HilbertCurve package provides a rather simple way to display the data in the form of Hilbert curve. It hides all the technical parts and users only need to think that they are adding graphics on a novel axis based on specifying positions.
Generally, customizing a Hilbert curve follows following steps:
hc = HilbertCurve(...) # initialize the curve
hc_points(hc, ...) # add points
hc_rect(hc, ...) # add rectangles
hc_polygon(hc, ...) # add polygons
hc_segments(hc, ...) # add lines
hc_text(hc, ...) # add text
HilbertCurve() is a constructor function and initializes the Hilbert curve. Following
example means initializing a Hilbert curve with level 4 which maps data ranging from 1 to 100.
The function returns a HilbertCurve class instance and it can be used to add more graphics later.
reference argument here is only used to show the structure of the curve.
hc = HilbertCurve(1, 100, level = 4, reference = TRUE)
By default, the Hilbert curve starts from the bottom left corner. The start position can be specifyed
by start_from option and the orientation of the first segment can be set by first_seg:
The curve can be though as a folded axis. When the coordinate for this folded axis is initialized, low-level graphics can be added by specifying the positions.
There are several ways to specify the “positions” of the data points. The most common way is
to construct a IRanges object:
library(IRanges)
x = sort(sample(100, 20))
s = x[1:10*2 - 1]
e = x[1:10*2]
ir = IRanges(s, e)
ir
## IRanges object with 10 ranges and 0 metadata columns:
## start end width
## <integer> <integer> <integer>
## [1] 1 4 4
## [2] 14 15 2
## [3] 16 31 16
## [4] 33 34 2
## [5] 40 44 5
## [6] 48 65 18
## [7] 67 73 7
## [8] 75 78 4
## [9] 86 87 2
## [10] 91 97 7
Here ir contains intervals which are composed by integers. In later sections,
you will see it is also possible to specify positions with numeric values and negative values.
There are two modes for adding points. Normally, intervals are always long in the curve and can not be sufficiently represented by single points, thus, by default, a list of e.g. circles split the intervals.
hc = HilbertCurve(1, 100, level = 4, reference = TRUE)
hc_points(hc, ir)
The number of circles used to represent the intervals can be controlled by np (number of points per segment).
np controls number of tiny segments that split every Hilbert curve segment (e.g. the first horizontal segment in the left bottom in the curve). Following plot is under np = 3.
hc = HilbertCurve(1, 16, level = 2, reference = TRUE, title = "np = 3")
hc_points(hc, x1 = 1, x2 = 2, np = 3)
Graphic parameters can be set by gp. Note under this mode, the size of points can only be controlled by np argument.
To make it more interesting, you can choose different shapes for the points. There are some pre-defined shapes
that you can choose from: “circle”, “square”, “triangle”, “hexagon”, “star”.
hc = HilbertCurve(1, 100, level = 4, reference = TRUE)
hc_points(hc, ir, np = 3, gp = gpar(fill = rand_color(length(ir))),
shape = sample(c("circle", "square", "triangle", "hexagon", "star"), length(ir), replace = TRUE))
In above figure, you may notice for some points, the color is more light in the ends. This is because the segments represented
by these light circles are not fully covered by user's input intervals, thus, averaging is applied here. E.g. if only
the half of the segment represented by the circle is covered by user's interval and the color for this circle is set to red,
then after the averaging, the color would be semi-red (#FF8080, an average between red and white). Averaging is very important when you visualize
the genome with zooming. You can find more detailed explanation in the Averaging section.
If np is set to 1 or NULL, there will be second mode for adding points that
the points are plotted at the center of every interval in ir.
In this case, size argument is used to control the size of the points. This mode is useful
if you have a lot of small intervals.
hc = HilbertCurve(1, 100, level = 4, reference = TRUE)
hc_points(hc, ir, np = NULL, size = unit(runif(length(ir)), "cm"), pch = 16)
Adding segments is quite straightforward. You can assign lwd to a large value to simulate
long and twisted rectangles.
hc = HilbertCurve(1, 100, level = 4, reference = TRUE)
hc_segments(hc, ir, gp = gpar(lwd = 5))
hc_rect() fills intervals by a list of squares. The squares always locate at the turning points
of the Hilbert curve and the width/height cannot be modified and it is automatically adjusted according
to the level of the curve.
There is a difference from hc_points() with setting shape to square. The number of squares per segment
is always 2 for hc_rect() while it can be any number for hc_points(). When the interval is long enough,
hc_rect() can completely fill the surrounding areas.
hc = HilbertCurve(1, 100, level = 4, reference = TRUE)
hc_rect(hc, ir, gp = gpar(fill = "#FF000080"))
As you can see some rectangles are not full red as well. It is also because of averaging. See Averaging sections for explanation.
Basically polygons are quite similar to the rectangles. The major difference is 1. borders can be set for irregular polygons; 2. there is only single color in one polygon while for rectangles, the color can change in the ends of the interval if the corresponding segment is not completely covered by the input interval.
hc = HilbertCurve(1, 100, level = 4, reference = TRUE)
hc_polygon(hc, ir, gp = gpar(fill = "#FF0000", col = "black"))
Text is always added at the center of each interval in ir. Additional settings such as
just and rot can also be set.
hc = HilbertCurve(1, 100, level = 4, reference = TRUE)
labels = sample(letters, length(ir), replace = TRUE)
hc_text(hc, ir, labels = labels, gp = gpar(fontsize = width(ir)*2+5))
With combination of these basic low-level graphic functions, complicated graphics can be easily made:
hc = HilbertCurve(1, 100, level = 4)
hc_segments(hc, IRanges(1, 100)) # This is an other way to add background line
hc_rect(hc, ir, gp = gpar(fill = rand_color(length(ir), transparency = 0.8)))
hc_polygon(hc, ir[c(1,3,5)], gp = gpar(col = "red"))
hc_points(hc, ir, np = 3, gp = gpar(fill = rand_color(length(ir))),
shape = sample(c("circle", "square", "triangle", "hexagon", "star"), length(ir), replace = TRUE))
hc_text(hc, ir, labels = labels, gp = gpar(fontsize = width(ir)*2+5, col = "blue", font = 2))
It doesn't matter if your positions are integers or not. Internally, adjustment is automatically applied.
When positions are not integers, you can specify the positions by x1 and x2.
All low-level graphical funtions accept x1 and x2.
hc = HilbertCurve(0.1, 0.8, level = 4, reference = TRUE)
hc_points(hc, x1 = c(0.15, 0.55), x2 = c(0.25, 0.65))
This is also useful to specify the positions with huge values which can not be represented by the IRagnes class (e.g. the summation of total length of human chromosomes).
# code not run when generating the vignette
hc = HilbertCurve(1, 1000000000000, level = 4, reference = TRUE)
hc_points(hc, x1 = 400000000000, x2 = 600000000000)
Negative positions are allowed as well.
# code not run when generating the vignette
hc = HilbertCurve(-100, 100, level = 4, reference = TRUE)
hc_points(hc, x1 = -50, x2 = 50)
The pixel mode can be thought as a high resolution version of hc_rect().
When the level is high (e.g. > 10), the whole 2D space will be almost completely filled by the curve and
it is impossible to add or visualize e.g. points on the curve. In this case, the 'pixel'
mode visualizes each tiny 'segment' as a pixel and maps values to colors. Internally, the whole plot
is represented as an RGB matrix and every time a new layer is added to the plot, the RGB matrix
will be updated according to the color overlay. When all the layers are added, normally a PNG figure is generated
directly from the RGB matrix. So the Hilbert
curve with level 11 will generate a PNG figure with 2048x2048 resolution. This is extremely
useful for visualize genomic data. E.g. If we make a Hilbert curve for human chromosome 1 with
level 11, then each pixel can represent 60bp (249250621/2048/2048) which is of very high resolution.
Under 'pixel' mode, every time a new layer is added, the image will be add to the interactive device as a rastered image.
hc = HilbertCurve(1, 100, level = 9, mode = "pixel")
hc_layer(hc, ir)
Since color is graphic representation to values, there is only one graphic setting col.
You can add more than one layers, and just remember to set transparent colors for the additional layers.
To map values to colors, users may try colorRamp2() function in circlize package to generate
a color mapping function. Another advantage of using colorRamp2() is it can be used to generate
the corresponding color legend.
col_fun = colorRamp2(c(0, 1), c("white", "red"))
x = sample(1000, 100)
value = runif(length(x))
hc = HilbertCurve(1, 1000, level = 9, mode = "pixel", title = "pixel mode")
hc_layer(hc, x1 = x, x2 = x+2, mean_mode = "absolute", col = col_fun(value))
hc_layer(hc, x1 = 750, x2 = 850, col = "#00000010")
Grid lines can be added to the plot for better distinguishing blocks in the Hilbert curve.
The 2D space will be split into 2^(grid_line-1) rows and 2^(grid_line-1) columns.
hc = HilbertCurve(1, 1000, level = 9, mode = "pixel", title = "pixel mode")
hc_layer(hc, x1 = x, x2 = x+2, mean_mode = "absolute", col = col_fun(value),
grid_line = 3)
Borders can be added by setting border to TRUE or a vector of colors to distinguish
different intervals.
hc = HilbertCurve(1, 1000, level = 9, mode = "pixel", title = "pixel mode")
hc_layer(hc, x1 = x, x2 = x+2, mean_mode = "absolute", col = col_fun(value), border = TRUE)
The Hilbert curve can be save as PNG figure by hc_png() with resolution 2^level x 2^level.
Note only the curve itself is exported.
# code not run, only for demonstration
hc_png(hc, file = "test.png")
As discussed before, under “pixel” mode, the Hilbert curve is stored in an RGB matrix, every time a new layer is added, the RGB values that correspond to the new input intervals will be updated according to the color and transparency of the new layer.
By default, the color overlay for layers is applied based on the transparency of the new layer.
Under “pixel” mode, each pixel is represented by red, green and blue colors for which the value is
between 0 and 1. When a new layer with transparency color is added, the overlayed RGB is calculated
as follows (r0, g0 and b0 correspond to the layer which is already added, r, g, b and alpha
correspond to the layer which is going to be added). The method is implemented in default_overlay() function.
r = r*alpha + r0*(1-alpha)
g = g*alpha + g0*(1-alpha)
b = b*alpha + b0*(1-alpha)
hc_layer() provides a overlay argument for which users can supply their own overlay method. This
may be easy to use but it is powerful for representing different features. In following example, we
change the red regions which are overlapped with the blue regions to green.
hc = HilbertCurve(1, 1000, level = 9, mode = "pixel", title = "pixel mode")
hc_layer(hc, x1 = x, x2 = x+2, mean_mode = "absolute")
hc_layer(hc, x1 = 750, x2 = 850, col = "#0000FF20",
overlay = function(r0, g0, b0, r, g, b, alpha) {
l = r0 > 0 # if the pixel is red
# red -> green, just switch red and green channel
tmp = r0[l]
r0[l] = g0[l]
g0[l] = tmp
# add to the curve
default_overlay(r0, g0, b0, r, g, b, alpha)
})
The self-defined overlay should accept seven arguments for which, r0, g0 and b0 correspond to RGB channles for the
layers which are already added, r, g, b and alpha correspond to the layer which are going to be added.
The elements of e.g. r, g, b only correspond to the pixels that are covered by the regions in the new layer.
If the colors are generated by the color mapping function which is generated by colorRamp2(),
col2value() function which is also from circlize package transforms back from colors to the original values
(it can be thought as the reversed function of colorRamp2()).
It is usefull to integrate with overlay to change the color theme if the color is from a continuous mapping.
In following plot, we change the color theme in the overlapped areas to white-blue. To do this,
we first select the pixels that correspond to the intersection of “red” areas and “grey” areas.
Since overlay is only applied to “grey” area and “red” area contains non-white pixels,
we only need to extract these non-white pixels inside the overlay function.
Then transform back to the original values by col2value() and finally change to
another color theme.
hc = HilbertCurve(1, 1000, level = 9, mode = "pixel", title = "pixel mode")
hc_layer(hc, x1 = x, x2 = x+2, mean_mode = "absolute", col = col_fun(value))
hc_layer(hc, x1 = 750, x2 = 850, col = "#00000010",
# remember r0, g0, ... only correspond to the pixels in the grey area
overlay = function(r0, g0, b0, r, g, b, alpha) {
# non-white areas
l = !(r0 == 1 & g0 == 1 & b0 == 1)
# original value
v = col2value(r0[l], g0[l], b0[l], col_fun = col_fun)
# new color theme
col_fun_new = colorRamp2(c(0, 1), c("white", "blue"))
col_new = col_fun_new(v, return_rgb = TRUE)
r0[l] = col_new[, 1]
g0[l] = col_new[, 2]
b0[l] = col_new[, 3]
default_overlay(r0, g0, b0, r, g, b, alpha)
})
In above example, actually you can implement such overlay by first split “red” regions into two parts
by whether they overlap with the “grey” regions. Then add the un-overlapped part, “grey” regions,
and overlapped regions as three independent layers. But the overlay option
provides an easier and more straightforward way to do it.
In later section, we will demonstrate using self-defined overlay method can effectively visualize the correspondance between H3K36me3 histone mark and gene body.
Title can be set by the title argument in HilbertCurve().
Legend can be passed to legend argument in HilbertCurve() as a grob object or a list of grob objects.
Basically, colors are the main aesthetic mappings to values, thus, Legend() function in ComplexHeatmap package
can be very helpful to create a legend grob. Also you can consider legendGrob() in grid package.
value = runif(length(ir))
col_fun = colorRamp2(c(0, 1), c("white", "red"))
legend1 = Legend(at = seq(0, 1, by = 0.2), col_fun = col_fun, title = "continuous")
legend2 = Legend(at = c("A", "B"), legend_gp = gpar(fill = c("#00FF0080", "#0000FF80")),
title = "discrete")
legend = list(legend1, legend2)
hc = HilbertCurve(1, 100, reference = TRUE, title = "points", legend = legend)
hc_points(hc, ir, np = 3, gp = gpar(fill = col_fun(value)))
hc_rect(hc, ir, gp = gpar(fill = sample(c("#00FF0020", "#0000FF20"), length(ir), replace = TRUE)))
ComplexHeatmap package also has a ColorMapping class which utilizes Legend() function to generate
legends. The advantage is the range and breaks on legends are automatically determined.
Under “pixel” mode, and when the curve is shown on the interactive device as raster image, title
and legends can be added as well. But if the plot is exported by hc_png(), there will be not
title and legends.
col_fun = colorRamp2(c(-2, 0, 2), c("green", "white", "red"))
breaks = seq(-2, 2, by = 2)
lgd1 = Legend(at = breaks, col_fun = col_fun, title = "style 1")
lgd2 = Legend(at = rev(breaks), legend_gp = gpar(fill = col_fun(rev(breaks))), title = "style 2")
cm = ColorMapping(col_fun = col_fun)
lgd3 = color_mapping_legend(cm, title = "style 3", plot = FALSE)
value = rnorm(length(x))
hc = HilbertCurve(1, 1000, level = 9, mode = "pixel", title = "pixel mode",
legend = list(lgd1, lgd2, lgd3))
hc_layer(hc, x1 = x, x2 = x+2, mean_mode = "absolute", col = col_fun(value))
Note: this “averaging” concept is very important. If you have unexpected plot, try other mean_mode option.
When using points or rectangles under “normal” mode, or using pixels under “pixel” mode, each point/rectangle/pixel is mapped to a small window in the genome. When overlapping certain genomic regions to the curve, and when the window is not full covered by the input regions, proper averaging method should be applied to summarize the value in the window.
Depending on different scenarios, HilbertCurve provides three metrics for averaging.
The overlapping model is illustrated in following plot. The red line in the bottom represents the small window on the Hilbert curve. Black lines on the top are the parts of input regions that overlap with the window. The thick lines indicate the intersected part between the input regions and the window.
For a window on the curve, \(n\) is the number of input regions which overlap with the window (it is 3 in the above plot), \(w_i\) is the width of the intersected segments (black thick lines), \(x_i\) is the value associated with the original regions.
The “absolute” method which is denoted as \(v_a\) and is simple calculated as the mean regardless of the width:
\[ v_a = \frac{\sum_i^n{x_i}}{n} \]
The “weighted” method which is denoted as \(v_w\) is the mean weighted by the width of intersections:
\[ v_w = \frac{\sum_i^n{x_iw_i}}{\sum_i^n{w_i}} \]
“Absolute” and “weighted” mode should be applied when background information is not of interest. E.g. when summarizing mean methylation in a small window, since methylation is only related with CpG sites while not other bases, non-CpG background should be ignored.
The “w0” mode is the weighted mean between the intersected parts and un-intersected parts:
\[ v_{w0} = \frac{v_wW + v_bW'}{W+W'} \]
for which \(W\) is sum of width of the intersected parts and \(W'\) is the sum of width for the un-intersected parts. \(V_b\) is the value corresponding to the background. E.g when averaging colors which are represented as numeric RGB values, the background value is set to 255 which corresponds to white.
This section gives several interesting examples.
Visualize rainbow colors:
col = rainbow(100)
hc = HilbertCurve(1, 100, level = 5)
hc_points(hc, x1 = 1:99, x2 = 2:100, np = 3, gp = gpar(col = col, fill = col))
or use the rectangles:
hc = HilbertCurve(1, 100, level = 5)
hc_rect(hc, x1 = 1:99, x2 = 2:100, gp = gpar(col = col, fill = col))
Reproduce the visualization for IPv4 address. The CIDR data is from http://www.iwik.org/ipcountry/.
library(ComplexHeatmap)
library(RColorBrewer)
load(system.file("extdata", "cidr_list.RData", package = "HilbertCurve"))
cidr_list = cidr_list[sapply(cidr_list, length) > 0]
country = rep(names(cidr_list), times = sapply(cidr_list, length))
ip = unlist(cidr_list, "r")
# convert ip address to numbers
mat = t(as.matrix(data.frame(lapply(strsplit(ip, "\\.|/"), as.numeric))))
start = mat[, 1]*256^3 + mat[, 2]*256^2 + mat[, 3]*256 + mat[, 4]
width = sapply(mat[, 5], function(x) strtoi(paste(rep(1, 32 - x), collapse = ""), base = 2))
# top 8 countries
col = structure(rep("grey", length(cidr_list)), names = names(cidr_list))
top8_rate = sort(tapply(width, country, sum), decreasing = TRUE)[1:8]/256^4
top8 = names(top8_rate)
col[top8] = brewer.pal(8, "Set1")
top8_rate = paste0(round(top8_rate*100), "%")
# this is the part of using HilbertCurve package
lgd = Legend(at = c(top8, "Others"), labels = c(paste(top8, top8_rate), "Others"),
legend_gp = gpar(fill = c(col[top8], "grey")), title = "Top8 contries")
hc = HilbertCurve(0, 256^4, start_from = "topleft", first_seg = "horizontal",
mode = "pixel", level = 9, legend = lgd)
hc_layer(hc, x1 = start, x2 = start + width, col = col[country])
Duration of Chinese dynasties. Data from http://www.360doc.com/content/11/1123/02/7829717_166641336.shtml.
load(system.file("extdata", "chinese_dynasty.RData", package = "HilbertCurve"))
detect_os = function() {
if (grepl('w|W', .Platform$OS.type)) {
os = "Windows"
} else {
if (grepl('darwin', version$os)) {
os = "MacOS"
} else {
os = "Linux"
}
}
return(os)
}
# default font family for Chinese under different OS
fontfamily = switch(detect_os(),
Windows = "SimSun",
MacOS = "Songti SC",
Linux = "Songti SC")
hc = HilbertCurve(min(chinese_dynasty[[2]]), max(chinese_dynasty[[3]]),
title = "Chinese dynasty (1122 B.C. ~ 1911 A.D.)",
title_gp = gpar(fontsize = 16, fontfamily = fontfamily))
hc_segments(hc, x1 = chinese_dynasty[[2]], x2 = chinese_dynasty[[3]],
gp = gpar(col = rand_color(nrow(chinese_dynasty), transparency = 0.2),
lwd = runif(nrow(chinese_dynasty), min = 1, max = 10)))
hc_text(hc, x1 = chinese_dynasty[[2]], x2 = chinese_dynasty[[3]], labels = chinese_dynasty[[1]],
gp = gpar(fontsize = (chinese_dynasty[[3]] - chinese_dynasty[[2]])/500 * 10 + 8,
year = seq(-1000, 2000, by = 100)
hc_text(hc, x1 = year, labels = ifelse(year < 0, paste0(-year, "BC"), year),
gp = gpar(fontsize = 8))
invisible(dev.off())
To make it easy with genomic data which is always stored as a data frame or a GRanges object,
the package provides specific class and functions to deal with it. GenomicHilbertCurve() initializes the
Hilbert curve by specifying chromosomes or specific background regions. After that, the data
frame or GRanges object which contains genomic intervals can be mapped to the curve.
Following functions are depatched to the GenomicHilbertCurve class, and the second argument
should be a data frame (which is in bed-format) or a GRanges object.
hc_points(hc, gr, ...)
hc_rect(hc, gr, ...)
hc_polygon(hc, gr, ...)
hc_segments(hc, gr, ...)
hc_text(hc, gr, ...)
hc_layer(hc, gr, ...)
Following illustrates several examples of making genome-level Hilbert curves.
The first example visualizes genes on chromosome 1 (RefSeq genes for human, hg19). Here random colors are used to distinguish different genes.
library(GenomicRanges)
load(system.file("extdata", "refseq_chr1.RData", package = "HilbertCurve"))
hc = GenomicHilbertCurve(chr = "chr1", level = 5, reference = TRUE,
reference_gp = gpar(lty = 1, col = "grey"), arrow = FALSE)
hc_segments(hc, g, gp = gpar(lwd = 6, col = rand_color(length(g))))
The conserved regions on human chromosome 1 between mouse and human or between zebrafish and human are downloaded from UCSC Table Browser. The parameters for downloading are:
clade: Mammal
genome: Human
assembly: Feb. 2009(GRCh37/hg19)
group: Comparative Genomics
= for mouse
track: Placental Chain/Net
table: Mouse Net (netMm10)
= for zebrafish
track: Vertebrate Chain/Net
table: Zebrafish Net(netDanRer7)
The “net” alignment which is used here shows the best alignment (the alignment algorithm allows longer gaps than traditional affine gap scoring systems) between each part in human genome and other genomes. For a detailed description of the alignment strategy, please go to UCSC Table Browser, and click describe table schema button.
In following example, the conservation data is mapped to a level 6 Hilbert curve under “normal” mode. Points are used as the graphic and each segment on the Hilbert curve is split by 3 points. In this case, each point on the curve represents approximately 30kb. Only chromosome 1 is visualized.
The point is fully red if the window which is represented by this point is completely covered by the conserved regions, and it is yellow if it is not covered by any region. Colors are interpolated linearly between red and yellow if it is partially covered by the conserved regions.
# for generating the legend
cm = ColorMapping(col_fun = colorRamp2(c(0, 1), c("yellow", "red")))
lgd = color_mapping_legend(cm, title = "Conservation", plot = FALSE,
at = c(0, 0.2, 0.4, 0.6, 0.8, 1),
labels = c("0%", "20%", "40%", "60%", "80%", "100%"))
chr1_len = 249250621
Conservation between human and mouse.
load(system.file("extdata", "mouse_net.RData", package = "HilbertCurve"))
seqlengths(mouse) = chr1_len # it is only used to extract the complement
nonmouse = gaps(mouse); nonmouse = nonmouse[strand(nonmouse) == "*"]
gr = c(mouse, nonmouse)
col = c(rep("red", length(mouse)), rep("yellow", length(nonmouse)))
hc = GenomicHilbertCurve(chr = "chr1", level = 6,
title = "Conservation between mouse and human on chr1",
legend = lgd)
hc_points(hc, gr, np = 3, gp = gpar(col = NA, fill = col))
Conservation between human and zebrafish.
load(system.file("extdata", "zebrafish_net.RData", package = "HilbertCurve"))
seqlengths(zebrafish) = chr1_len
nonzebrafish = gaps(zebrafish); nonzebrafish = nonzebrafish[strand(nonzebrafish) == "*"]
gr = c(zebrafish, nonzebrafish)
col = c(rep("red", length(zebrafish)), rep("yellow", length(nonzebrafish)))
hc = GenomicHilbertCurve(chr = "chr1", level = 6,
title = "Conservation between zebrafish and human on chr1",
legend = lgd)
hc_points(hc, gr, np = 3, gp = gpar(col = NA, fill = col))
Compareing these two plots, we have following conclusions:
The idea of visualizing sequencing conservation through the Hilbert curve is from here.
Following figure visualizes GC percent on chromosome 1, under “normal” mode. The GC content per 1KB window
is calculated by hgGcPercent.bin binary which is downloaded from http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/.
df = read.table(pipe("awk '$1==\"chr1\"' ~/HilbertCurveTest/hg19_gc_percent_window1000.bed"))
col_fun = colorRamp2(quantile(df[[5]], c(0.1, 0.5, 0.9)), c("green", "#FFFFCC", "red"))
cm = ColorMapping(col_fun = col_fun)
lgd = color_mapping_legend(cm, title = "GC percent", plot = FALSE,
at = c(300, 400, 500, 600),
labels = c("30%", "40%", "50%", "60%"))
hc = GenomicHilbertCurve(chr = "chr1", level = 6, legend = lgd)
hc_points(hc, df, np = 3, gp = gpar(fill = col_fun(df[[5]]), col = col_fun(df[[5]])))
hc_rect(hc, reduce(g), gp = gpar(fill = "#00000020", col = NA))
Or visualize GC percent on chromosome 1, under “pixel” mode (you may see the difference between “normal” mode and “pixel” mode here):
hc = GenomicHilbertCurve(chr = "chr1", level = 9, mode = "pixel", legend = lgd)
hc_layer(hc, df, col = col_fun(df[[5]]))
hc_layer(hc, reduce(g), col = "#00000020")
# or you can only save the Hilbert curve part as a PNG file
# hc_png(hc, file = "gc_percent_chr1.png")
Background is not necessary to be the whole chromosome, it can also be self-defined regions.
The background can be specified as a GRanges object and pass to background argument.
In following example, only the first half part of chromosome 1 is used to initialize the curve.
Note: when using background, one chromosome can only exist in one row in background.
background = GRanges(seqnames = "chr1", ranges = IRanges(1, ceiling(chr1_len/2)))
hc = GenomicHilbertCurve(background = background, level = 9, mode = "pixel", legend = lgd,
title = "First half of chromosome 1")
hc_layer(hc, df, col = col_fun(df[[5]]))
hc_layer(hc, reduce(g), col = "#00000020")
# or you can only save the Hilbert curve part as a PNG file
# hc_png(hc, file = "gc_percent_half_chr1.png")
Different modifications (e.g. methylation, acetylation) of the histones affect the chromatin-DNA interaction, thus play roles in transcription regulation. Different types of modifications relates to different types of gene regulation. E.g. H3H4me3 modification is found in actively transcribed promoters. ChIP-sequencing (ChIPSeq) utilizes highthroughput DNA sequencing technology to identify status of chromatin states genome-wide, thus it provides a way to study gene regulation in a global aspect.
In this section, we visualize four types of histone modifications (H3K27ac, H3K36me3, H3K4me3, H3K9me3). The ChIPSeq data are downloaded from Roadmap (http://genboree.org/EdaccData/Release-9/sample-experiment/Lung/, The bed files are alignments of reads, you need to convert to the basepair or window-based coverage before using following R commands). Following files for four histone modifications are used to visualize:
UCSD.Lung.H3K27ac.STL002.bed
UCSD.Lung.H3K36me3.STL002.bed
UCSD.Lung.H3K4me3.STL002.bed
UCSD.Lung.H3K9me3.STL002.bed
Since we are going to plot more than one histome marks, the code for plotting are wrapped as a simple function:
library(GetoptLong)
plot_histone_mark = function(mark) {
df = read.table(pipe(qq("awk '$5>0 && $1==\"chr1\"' ~/HilbertCurveTest/UCSD.Lung.@{mark}.STL002.bed")),
sep = "\t")
col_fun = colorRamp2(c(0, quantile(df[[5]], 0.99)), c("white", "red"))
cm = ColorMapping(col_fun = col_fun)
lgd = color_mapping_legend(cm, title = "Intensity", plot = FALSE)
cm2 = ColorMapping(level = c(mark, "gene"), color = c("#FF0000", "#CCCCCC"))
lgd2 = color_mapping_legend(cm2, title = "Layer", plot = FALSE)
hc = GenomicHilbertCurve(chr = "chr1", level = 9, mode = "pixel",
title = qq("Intensity of @{mark} mark on chr1"), legend = list(lgd, lgd2))
hc_layer(hc, df, col = col_fun(df[[5]]))
hc_layer(hc, reduce(g), col = "#00000010")
# or you can only save the Hilbert curve part as a PNG file
# hc_png(hc, qq("@{mark}_chr1.png"))
}
In above code, intensities of histone modifications are mapped to a level 9 Hilbert curve so that each pixel approximately represents a window of 950bp. In each plot, there is an additional grey layer which represents the regions of genes (RefSeq genes). For the regions which are overlapped with gene bodies, the color theme is changed to white-purple, which helps to visualize the correspondance between histone modifications and gene bodies.
H3K27ac is a mark for active enhancers which is narrow and sharp. The Hilbert curve shows this attributes and also shows enhancers may exist in form of clusters.
plot_histone_mark("H3K27ac")
H3K36me3 is a mark for actively transcribed gene bodies. The Hilbert curve shows that basically most of H3K36me3 modification with high intensity exists in gene bodies (the purple regions).
plot_histone_mark("H3K36me3")
H3K4me3 is a mark for TSS of actively transcribed genes which is also narrow and sharp. The Hilbert curve confirms this and also shows the size of marks are quite consistent.
plot_histone_mark("H3K4me3")
H3K9me3 is a mark for repressed genes. The Hilbert curve shows that H3K9me3 modications spread over huge regions in the chromosome.
plot_histone_mark("H3K9me3")
When there are more than one layers added and users want to see the correspondance between different genomic features, they can define a color overlay function to enhance the visual effects of the overlapping areas. In following example, when regions for H3K36me3 mark are overlapped with gene bodies, the color theme is changed to white-purple.
df = read.table(pipe("awk '$5>0 && $1==\"chr1\"' ~/HilbertCurveTest/UCSD.Lung.H3K36me3.STL002.bed"),
sep = "\t")
col_fun = colorRamp2(c(0, quantile(df[[5]], 0.99)), c("white", "red"))
col_fun_new = colorRamp2(c(0, quantile(df[[5]], 0.99)), c("white", "purple"))
cm = ColorMapping(col_fun = col_fun)
lgd = color_mapping_legend(cm, title = "Intensity", plot = FALSE)
cm2 = ColorMapping(level = c("H3K36me3", "overlap", "gene"), color = c("#FF0000", "purple", "#CCCCCC"))
lgd2 = color_mapping_legend(cm2, title = "Layer", plot = FALSE)
hc = GenomicHilbertCurve(chr = "chr1", level = 9, mode = "pixel",
title = "Intensity of H3K36me3 mark on chr1", legend = list(lgd, lgd2))
hc_layer(hc, df, col = col_fun(df[[5]]))
hc_layer(hc, reduce(g), col = "#00000010",
overlay = function(r0, g0, b0, r, g, b, alpha) {
l = !(r0 == 1 & g0 == 1 & b0 == 1)
v = col2value(r0[l], g0[l], b0[l], col_fun = col_fun)
col_new = col_fun_new(v, return_rgb = TRUE)
r0[l] = col_new[, 1]
g0[l] = col_new[, 2]
b0[l] = col_new[, 3]
default_overlay(r0, g0, b0, r, g, b, alpha)
})
# or you can only save the Hilbert curve part as a PNG file
# hc_png(hc, "H3K36me3_chr1_overlap.png")
Next figure visualizs methylation on human chromosome 1. Blue corresponds to un-methylation and red corresponds to full-methylation.
One thing which is very important here is that methylation is always measured at single CpG
sites, so the mode for averaging should be set to absolute in order to sumarize mean methylation values only on CpG sites.
Data are from http://genboree.org/EdaccData/Release-9/sample-experiment/Lung/.
The methylation plot shows quite clear patterns for un-methylated regions which are small and sharp, fully methylated regions and intermediate methylated regions which are represented as large blocks.
df = read.table(pipe("awk '$1==\"chr1\"' ~/HilbertCurveTest/UCSD.Lung.Bisulfite-Seq.STL002.bed"),
sep = "\t")
col_fun = colorRamp2(c(0, 0.5, 1), c("blue", "white", "red"))
cm = ColorMapping(col_fun = col_fun)
lgd = color_mapping_legend(cm, title = "Methylation", plot = FALSE)
hc = GenomicHilbertCurve(chr = "chr1", level = 9, mode = "pixel", legend = lgd)
hc_layer(hc, df, col = col_fun(df[[5]]), mean_mode = "absolute")
hc_layer(hc, reduce(g), col = "#00000010")
# or you can only save the Hilbert curve part as a PNG file
# hc_png(hc, file = 'methylation_chr1.png')
We demonstrated how to visualize one single chromosome through Hilbert curve, but sometimes
we also want to put all chromosomes into one plot to get a full view of the genome.
One solution is to construct a 'huge fake' chromosome which merges all real chromosomes. GenomicHilbertCurve()
makes it easy. You can specify multiple chromosomes by sending a vector to chr argument or specify more
than one background intervals in background argument.
In following examples, copy number loss and gain for 22 human chromosomes are visualized. Also color for the overlapping
regions between layer for gain events and layer for loss events is changed to purple by defining overlay function.
Data is from Database of Genomic Variants, CNV map.
hc = GenomicHilbertCurve(chr = paste0("chr", 1:22), level = 9, mode = "pixel")
df_gain = read.table("~/HilbertCurveTest/Stringent.Gain.hg19.2015-02-03.txt",
header = TRUE, stringsAsFactors = FALSE)
hc_layer(hc, df_gain, col = "red")
df_loss = read.table("~/HilbertCurveTest/Stringent.Loss.hg19.2015-02-03.txt",
header = TRUE, stringsAsFactors = FALSE)
hc_layer(hc, df_loss, col = "green", grid_line = 3, grid_line_col = "grey",
overlay = function(r0, g0, b0, r, g, b, alpha) {
l = !(r0 == 1 & g0 == 1 & b0 == 1)
r[l] = 160/255
g[l] = 32/255
b[l] = 240/255
list(r, g, b)
})
A map which shows the chromosome positions in Hilbert curve is very necessary for knowing which part in the curve represents which chromosome.
hc_map(hc)
The map can be overlayed to the Hilbert curve for easy correspondance.
hc = GenomicHilbertCurve(chr = paste0("chr", 1:22), level = 9, mode = "pixel")
hc_layer(hc, df_gain, col = "red")
hc_layer(hc, df_loss, col = "green",
overlay = function(r0, g0, b0, r, g, b, alpha) {
l = !(r0 == 1 & g0 == 1 & b0 == 1)
r[l] = 160/255
g[l] = 32/255
b[l] = 240/255
list(r, g, b)
})
hc_map(hc, add = TRUE, fill = rand_color(22, transparency = 0.8))
If colors of chromosomes defuse the colors in the original Hilbert curve, you can only draw borders of chromosomes.
hc = GenomicHilbertCurve(chr = paste0("chr", 1:22), level = 9, mode = "pixel")
hc_layer(hc, df_gain, col = "red")
hc_layer(hc, df_loss, col = "green",
overlay = function(r0, g0, b0, r, g, b, alpha) {
l = !(r0 == 1 & g0 == 1 & b0 == 1)
r[l] = 160/255
g[l] = 32/255
b[l] = 240/255
list(r, g, b)
})
hc_map(hc, add = TRUE, fill = NA, border = "grey")
If you want to compare several plots simutaneously, you can use grid.layout()
to put them together. Remember to set newpage to FALSE in HilbertCurve() or GenomicHilbertCurve().
plot_curve = function(column, ...) {
cm = ColorMapping(levels = c("gain", "loss", "both"), color = c("red", "green", "purple"))
hc = GenomicHilbertCurve(chr = paste0("chr", 1:22), level = 9, mode = "pixel",
title = qq("CNV for @{column}"), ...) ## `qq()` is from the GetoptLong package
df = read.table("~/HilbertCurveTest/Stringent.Gain.hg19.2015-02-03.txt", header = TRUE, stringsAsFactors = FALSE)
df = df[df[[column]] > 0, , drop = FALSE]
hc_layer(hc, df, col = "red")
df = read.table("~/HilbertCurveTest/Stringent.Loss.hg19.2015-02-03.txt", header = TRUE, stringsAsFactors = FALSE)
df = df[df[[column]] > 0, , drop = FALSE]
hc_layer(hc, df, col = "green",
overlay = function(r0, g0, b0, r, g, b, alpha) {
l = !(r0 == 1 & g0 == 1 & b0 == 1)
r[l] = 160/255
g[l] = 32/255
b[l] = 240/255
list(r, g, b)
})
hc_map(hc, add = TRUE, fill = NA, border = "grey")
}
pn = c("African", "Asian", "European")
pushViewport(viewport(layout = grid.layout(nrow = 1, ncol = 3)))
for(i in seq_along(pn)) {
pushViewport(viewport(layout.pos.row = 1, layout.pos.col = i))
plot_curve(pn[i], newpage = FALSE)
upViewport()
}
upViewport()
sessionInfo()
## R version 3.5.1 Patched (2018-07-12 r74967)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 16.04.5 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.8-bioc/R/lib/libRblas.so
## LAPACK: /home/biocbuild/bbs-3.8-bioc/R/lib/libRlapack.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
## [4] LC_COLLATE=C LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
## [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 parallel grid stats graphics grDevices utils datasets methods
## [10] base
##
## other attached packages:
## [1] GetoptLong_0.1.7 GenomicRanges_1.34.0 GenomeInfoDb_1.18.0 RColorBrewer_1.1-2
## [5] IRanges_2.16.0 S4Vectors_0.20.0 BiocGenerics_0.28.0 ComplexHeatmap_1.20.0
## [9] HilbertVis_1.40.0 lattice_0.20-35 circlize_0.4.4 HilbertCurve_1.12.0
## [13] knitr_1.20 markdown_0.8
##
## loaded via a namespace (and not attached):
## [1] XVector_0.22.0 magrittr_1.5 zlibbioc_1.28.0 colorspace_1.3-2
## [5] rjson_0.2.20 stringr_1.3.1 highr_0.7 tools_3.5.1
## [9] png_0.1-7 GenomeInfoDbData_1.2.0 GlobalOptions_0.1.0 bitops_1.0-6
## [13] RCurl_1.95-4.11 shape_1.4.4 evaluate_0.12 stringi_1.2.4
## [17] compiler_3.5.1