track_bedgraph {rGenomeTracks} | R Documentation |
Generate genome_track object from bedgraph files.
track_bedgraph( file, title = NULL, height = 2, overlay_previous = "no", orientation = NULL, color = "#1f78b4", alpha = 1, max_value = NULL, min_value = NULL, use_middle = FALSE, show_data_range = TRUE, type = "fill", negative_color = NULL, nans_to_zeros = FALSE, summary_method = NULL, number_of_bins = 700, transform = "no", log_pseudocount = 0, y_axis_values = "transformed", second_file = NULL, operation = "file", grid = FALSE, rasterize = FALSE )
file |
String. The location of the track file |
title |
String. If specificed, the title of the track to be displayed. |
height |
Numeric. The height of the plotted track in cm. Default is 2. See notes. |
overlay_previous |
String. Options are "no" (default) or "yes" or "share-y". |
orientation |
String. Default is NULL. Other option is "inverted". |
color |
String. Hex color or string color. Default is "#1f78b4". |
alpha |
Numeric variable between 0 and 1 to indicate level of transparancy. Default is 1. |
max_value |
Numeric. Default is NULL. The max value cut-off for the numeric column. |
min_value |
Numeric. Default is NULL. The max value cut-off for the numeric column. |
use_middle |
Boolean. Default is FALSE. |
show_data_range |
Boolean. Default is TRUE. |
type |
String. Options are "fill" (default),"line", "points". |
negative_color |
Hex color or string to indicate color of negative values. Default is NULL. |
nans_to_zeros |
Boolean. To convert empty values to zeros, set this to TRUE. Default is FALSE. |
summary_method |
String. summary_method applied over bin range. This parameter is set to NULL. See details for options. |
number_of_bins |
Numeric value to indicate summary method used over the bin range. Default is 700 |
transform |
String to indicate type of transformation applied. Default is "no". |
log_pseudocount |
Numeric. Default is 0. |
y_axis_values |
String with two options "transformed" (default) or "original". |
second_file |
Path for another file to be included in operations. This parameter is not set by default. |
operation |
Default is set to "file". See details. |
grid |
Boolean. Default is FALSE. |
rasterize |
Boolean. Default is FALSE. |
summary_method parameter can be choosen to be by "mean", "average", "max",
"min", "stdev", "dev", "coverage", "cov" or "sum".
Tranform paramter options are "no" (default) or "log", "log1p", "-log", "log2" or "log10".
'log1p': transformed_values = log(1 + initial_values)
'log': transformed_values = log(log_pseudocount + initial_values)
'log2': transformed_values = log2(log_pseudocount + initial_values)
'log10': transformed_values = log10(log_pseudocount + initial_values)
'-log': transformed_values = log(log_pseudocount + initial_values)
To compute operations on the fly on the file or between 2 bedgraph files,
you can tweak operation parameter, it should contains file or
file and second_file. It is adviced to use nans_to_zeros = TRUE
to
avoid unexpected results. Example value for operation are "0.89 * file",
"- file", "file - second_file", "log2((1 + file) / (1 + second_file))" and
"max(file, second_file)"
to add the preferred line width or point size : type = "line:lw" where lw (linewidth) is numeric value.
Like type = "line:0.5"
and type = "points:0.5"
By default the bedgraph is plotted at the base pair resolution.
This can lead to very large pdf/svg files. If plotting large regions.
If you want to decrase the size of your file.
You can either rasterize the bedgraph profile by using: rasterize = TRUE
genome_track
fontsize
parameter can be overriden by the same argument in plot_gtracks()
height
parameter will be ignored if overlay_previous
is set.
Omar Elashkar
bg_dir <- system.file("extdata", "GSM3182416_E12DHL_WT_Hoxd11vp.bedgraph.gz", package = "rGenomeTracks" ) bed_genes_dir <- system.file("extdata", "HoxD_cluster_regulatory_regions_mm10.bed", package = "rGenomeTracks" ) bg <- track_bedgraph(bg_dir, color = "green", height = 5, max_value = 10) bg_middle <- track_bedgraph(bg_dir, use_middle = TRUE, color = "blue", height = 5, max_value = 10 ) bed_genes <- track_bed(bed_genes_dir, title = "Regulatory regions", , color = "red", height = 3 ) tracks <- track_x_axis(where = "top") + bg + bg_middle + bed_genes ## Not run: plot_gtracks(tracks, chr = 2, start = 738 * 10^5, end = 750 * 10^5, trackLabelFraction = 0.2 ) ## End(Not run)