plot_gtracks {rGenomeTracks} | R Documentation |
This is a generic function used to plot genome_track
objects.
plot_gtracks( obj, chr, start, end, dir = NULL, plot = TRUE, verbose = FALSE, dpi = 100, title = NULL, fontsize = NULL, width = 40, height = NULL, trackLabelFraction = 0.05, trackLabelHAlign = "left", ... ) ## S4 method for signature 'genome_track' plot_gtracks( obj, chr, start, end, dir = NULL, plot = TRUE, verbose = FALSE, dpi = 100, title = NULL, fontsize = NULL, width = 40, height = NULL, trackLabelFraction = 0.05, trackLabelHAlign = "left", ... )
obj |
genome_track object. Define all tracks to be plotted. |
chr |
String or numeric value to indicate the chromosome desire. |
start |
Numeric. Starting position of plotting on the defined chromosome. |
end |
Numeric. Starting position of plotting on the defined chromosome. |
dir |
String. Default is NULL. If defined, a string to directory and extension to which image is exported. Extension could be png, svg or pdf. |
plot |
Boolean. Default if TRUE. If FALSE, plot will not be generated, only exported. |
verbose |
If TRUE, print command that will be passed to pyGenomeTracks. |
dpi |
Numeric. Default is 100 |
title |
String. Title of the generated plot. Default is NULL. |
fontsize |
If set, global fontsize value overrides individual tracks.R . argument of all tracks passed. |
width |
Numeric. The width of the plot. Default is 40 |
height |
Numeric. Height of the plot. Default is NULL to set is based on tracks height. |
trackLabelFraction |
Numeric. Default is 0.05. |
trackLabelHAlign |
String. Position of labels aligment. Options are "left", "right" or "center". Default is "left". |
... |
Extra arguments to be passed for generic plot(). |
None
None
For this function to run, you need pyGenomeTracks installed in R's loading enviroment. If not, please run install_pyGenomeTracks()
Omar Elashkar
Omar Elashkar
## Not run: # Get example data directories # Download h5 example ah <- AnnotationHub() query(ah, "rGenomeTracksData") h5_dir <- ah[["AH95901"]] tads_dir <- system.file("extdata", "tad_classification.bed", package = "rGenomeTracks" ) arcs_dir <- system.file("extdata", "links2.links", package = "rGenomeTracks") bw_dir <- system.file("extdata", "bigwig2_X_2.5e6_3.5e6.bw", package = "rGenomeTracks") # # Create HiC track from HiC matrix h5 <- track_hic_matrix( file = h5_dir, depth = 250000, min_value = 5, max_value = 200, transform = "log1p", show_masked_bins = FALSE ) # Create TADS track tads <- track_domains( file = tads_dir, border_color = "black", color = "none", height = 5, line_width = 5, show_data_range = FALSE, overlay_previous = "share-y" ) # Create arcs track arcs <- track_links( file = arcs_dir, links_type = "triangles", line_style = "dashed", overlay_previous = "share-y", color = "darkred", line_width = 3, show_data_range = FALSE ) # Create bigwig track bw <- track_bigwig( file = bw_dir, color = "red", max_value = 50, min_value = 0, height = 4, overlay_previous = "yes", show_data_range = FALSE ) # Create one object from HiC, arcs and bigwid tracks <- h5 + arcs + bw # Plot the tracks plot_gtracks(tracks, chr = "X", start = 25 * 10^5, end = 31 * 10^5) # Plot HiC, TADS and bigwig tracks plot_gtracks(h5 + tads + bw, chr = "X", start = 25 * 10^5, end = 31 * 10^5) ## End(Not run)