GViz.jl

GViz.jl

Purpose
Examples
API

Purpose

GViz.jl is a julia library to visualize genomic data using tracks. The library is implemented on top of the Cairo vector graphics library.

The user specifies track objects

GenomicAxis
DataTrack (for x, y data)
GeneTrack (for genes)

that are plotted to a PDF file using plotTracks.

Internally, each display consists of a number of nested reference frames. Each reference frame has a coordinate system and an environment for parameters. Both attributes and data are stored in the environment. A child reference frame is mapped onto its parent reference frame using scaling and translation transformations. When trying to look up an attribute in a reference frame's environment that does not exists there, its parents' environments are checked recursively.

Examples

using GViz

chrom_ = "chr20"
bpStart_ = 31400000
bpEnd_ = 31550229

gp = GenomicAxis(;height=1cm, margin_top = 8mm)
gt = GeneTrack(chrom_, bpStart_, bpEnd_)
dt = DataTrack(x = range(bpStart_, bpEnd_, length=1000), y = rand(1000),
               ymin = -0.05, ymax = 1.05, title = "Random data", height=5cm )

plotTracks([gp, dt, gt, gp], "/tmp/test1.pdf", bpStart_, bpEnd_;
	   defaultparams..., width=20cm)

using GViz
using GorJulia

chrom_ = "chr20"
bpStart_ = 31400000
bpEnd_ = 31550229

gp = GenomicAxis(;height=1cm, margin_top = 8mm)

gt = GeneTrack(chrom_, bpStart_, bpEnd_)

hmeth = GorFile(GViz.pkgpath("data", "PofO_ASM.gor");
                first = (chrom_, bpStart_), last = (chrom_, bpEnd_)) |> Tables.columns

hmt = DataTrack(x = hmeth[:Pos],
                layers = [Dict(:y => hmeth[:mfrac], :fill => "blue"),
                          Dict(:y => hmeth[:pfrac], :fill => "red")],
                ymin=0, ymax = 1, title="ASM",
                size=1, margin_top=0mm, color="white")

zt = DataTrack(x = hmeth[:Pos], y = -log10.(hmeth[:pval]),
               ymin=0, ymax = 20, title="ASM -log10(p)",
               size=1, margin_top=0mm, geom = :col, color = "darkblue")

plotTracks([gp, zt, hmt, gt], "/tmp/test2.pdf", bpStart_, bpEnd_; defaultparams..., width=25cm)

API

GViz.GenomicAxis — Type

GenomicAxis(;params...)

Create a genomic axis for the track plots.

Parameters

:axis_line_width
:axis_color
:axis_font
:axis_tick_length
:width width of track
:height height of track
:margin_top
:margin_bottom
:margin_left
:margin_right

source

GViz.DataTrack — Type

DataTrack(;params...)

Create a data track consisting of one or multiple layers.

Layer parameters

:x
:y
:color
:fill
:size
:linetype
:alpha
:shape
- :asterisk
- :circle
- :cross
- :diamond
- :dot
- :plus
- :square
- :triangle
- :down-triangle
- :right-triangle
- :left-triangle
:geom
- :point
- :line
- :col

If a single layer is used, the parameters are specified directly. If multiple layers are used, the parameters for each layer are specified in a separate dictionary, and a vector of layer dictionaries can be supplied as parameter :layers.

Track parameters

The following parameters affect the track as a whole

:title track title
:title_color
:title_font
:ymin minimum y-value to plot, or nothing
:ymax maximum y-value to plot, or nothing
:axis_line_width
:axis_color
:axis_font
:axis_tick_length
:base_line_y y-coordinates for horizontal line, or nothing
:base_line_color
:base_line_width
:width width of track
:height height of track
:margin_top
:margin_bottom
:margin_left
:margin_right

source

GViz.GeneTrack — Function

GeneTrack(chrom, bpStart, bpEnd; 
          gtf = GViz.pkgpath("data", "gencode.v35.annotation.gtf.bgz"),
          params...)

Create a track with genes based on GTF file gtf.

Parameters

:gtf path to tabix-indexed GTF file with genes
:feature_label_spacing
:feature_label_font
:feature_label_color
:feature_height
:feature_fill
:title track title
:title_color
:title_font
:width width of track
:height height of track
:margin_top
:margin_bottom
:margin_left
:margin_right

source

GViz.plotTracks — Function

plotTracks(tracks::Vector{T}, path, xmin, xmax;
                track_spacing = 5mm, params...)

Plot tracks into PDF file at path.

source