gtrellis_layout: Initialize genome-level Trellis layout

In eilslabs/gtrellis: Genome Level Trellis Layout

Description

Initialize genome-level Trellis layout

Usage

gtrellis_layout(data = NULL, category = NULL,
    species = NULL, nrow = NULL, ncol = NULL,
    n_track = 1, track_height = 1, track_ylim = c(0, 1),
    track_axis = TRUE, track_ylab = "", title = NULL,
    xlab = "Genomic positions", xaxis = TRUE, xaxis_bin = NULL,
    equal_width = FALSE, compact = FALSE, border = TRUE, asist_ticks = TRUE,
    xpadding = c(0, 0), ypadding = c(0, 0), gap = unit(1, "mm"),
    byrow = TRUE, newpage = TRUE, add_name_track = FALSE,
    name_fontsize = 10, name_track_fill = "#EEEEEE",
    add_ideogram_track = FALSE, ideogram_track_height = unit(2, "mm"),
    axis_label_fontsize = 6, lab_fontsize = 10, title_fontsize = 16,
    legend = list(), legend_side = c("right", "bottom"),
    padding = unit(c(2, 2, 2, 2), "mm"), remove_chr_prefix = FALSE)

Arguments

data	a data frame with at least three columns. The first three columns should be genomic categories (e.g. chromosomes), start positions and end positions. This data frame is used to extract ranges for each genomic category (minimal and maximal positions are taken as the range in the corresponding category).
category	subset of categories. It is also used for ordering.
species	Abbreviations of species. e.g. hg19 for human, mm10 for mouse. If this value is specified, the function will download chromInfo.txt.gz from UCSC ftp automatically. Short scaffolds will be removed if they have obvious different length as others. Non-normal chromosomes will also be detected and removed. Sometimes this detection is not always correct and if you find chromosomes shown on the plot is not what you expect, set category manually. The argument is passed to read.chromInfo.
nrow	Number of rows in the layout.
ncol	Number of columns in the layout.
n_track	Number of tracks in each genomic category.
track_height	height of tracks. It should be numeric which means the value is relative and will be scaled into percent, or a unit object.
track_ylim	ranges on y axes of tracks. The value can be a vector of length two which means all tracks share same y ranges, or a matrix with two columns, or a vector of length 2*n_track which will be coerced into the two-column matrix by rows.
track_axis	whether show y axes for tracks. The value is logical that can be either length one or number of tracks.
track_ylab	labels for tracks on y axes. The value can be either length one or number of tracks.
title	title of the plot.
xlab	labels on x axes.
xaxis	whether show x axes.
xaxis_bin	bin size for x axes.
equal_width	whether all columns in the layout have the same width. If TRUE, short categories will be extended according to the longest category.
compact	For the catgories which are put in a same row, will they be put compactly without being aligned by columns.
border	whether show borders.
asist_ticks	if axes ticks are added on one side in rows or columns, whether add ticks on the other sides.
xpadding	padding on x axes in each cell. Numeric value means relative ratio corresponding to the cell width. Use I to set it as absolute value which is measured in the data viewport (the coordinate system corresponding to the real data). Currently you cannot set it as a unit object.
ypadding	padding on y axes in each cell. Only numeric value is allowed currently.
gap	0 or a unit object. If it is length two, the first element corresponds to the gaps between rows and the second corresponds to the gaps between columns.
byrow	arrange categories (e.g. chromosomes) by rows or by columns in the layout.
newpage	whether call grid.newpage to create a new page.
add_name_track	whether add a pre-defined name track (insert before the first track). The name track is simply a track which only contains text. The default style of the name track is simple, but users can self define their own by add_track.
name_fontsize	font size for text in the name track. Note the font size also affects the height of name track.
name_track_fill	filled color for name track.
add_ideogram_track	whether to add a pre-defined ideogram track (insert after the last track). If the cytoband data for specified species is not available, this argument is ignored. The ideogram track simply contains rectangles with different colors, implemented by add_track.
ideogram_track_height	Height of ideogram track. The value should be a unit object.
axis_label_fontsize	font size for axis labels.
lab_fontsize	font size for x-labels and y-labels.
title_fontsize	font size for title.
legend	a grob object, or a list of grob objects.
legend_side	side of the legend
padding	padding of the plot. Elements correspond to bottom, left, top, right paddings.
remove_chr_prefix	if chromosome names start with 'chr', whether to remove it.

Details

Genome-level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. The gtrellis_layout function arranges genomic categories on the plot in a quite flexible way. Then users apply add_track to add self-defined graphics to the plot track by track.

For more detailed demonstration of the function, please refer to the vignette.

Value

No value is returned.

Author(s)

Zuguang Gu <[e-mail]>

See Also

add_track, add_ideogram_track

Examples

gtrellis_layout()
gtrellis_layout(ncol = 5)
gtrellis_layout(n_track = 3, ncol = 4)

# for more examples, please go to the vignette

eilslabs/gtrellis documentation built on May 16, 2019, 1:25 a.m.