track_bigwig {rGenomeTracks} | R Documentation |
Create genome_track object from bigwig file.
track_bigwig( file, title = NULL, height = 2, overlay_previous = "no", orientation = NULL, color = "#1f78b4", alpha = 1, max_value = NULL, min_value = NULL, show_data_range = TRUE, type = "fill", negative_color = NULL, nans_to_zeros = FALSE, summary_method = "mean", number_of_bins = 700, transform = "no", log_pseudocount = 0, y_axis_values = "transformed", second_file = NULL, operation = "file", grid = 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. |
overlay_previous |
String. Options are "no" (default) or "yes" or |
orientation |
String. Set to "inverted" to make the track upside down. Default is NULL. |
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. |
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. |
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)"
None
Like type = "line:0.5"
and type = "points:0.5"
Omar Elashkar
bw_dir <- system.file("extdata", "bigwig2_X_2.5e6_3.5e6.bw", package = "rGenomeTracks" ) mean_bw <- track_bigwig( file = bw_dir, color = "gray", type = "point:1", summary_method = "mean", number_of_bins = 300, max_value = 200, min_value = -5 ) min_bw <- track_bigwig( file = bw_dir, color = "blue", type = "line:1", summary_method = "min", number_of_bins = 300, overlay_previous = "share-y", show_data_range = FALSE, max_value = 200, min_value = -5 ) max_bw <- track_bigwig( file = bw_dir, color = "red", type = "line:1", summary_method = "max", number_of_bins = 300, overlay_previous = "share-y", show_data_range = FALSE, max_value = 200, min_value = -5 ) hlines <- track_hlines( y_values = "10, 150", overlay_previous = "share-y", color = "blue", line_style = "dotted" ) ## Not run: plot_gtracks(mean_bw + min_bw + max_bw + hlines, chr = "X", start = 27 * 10^5, end = 31 * 10^5) ## End(Not run)