batchHubGenerator: batchHubGenerator
In msubirana/ucschubgenerator: What the Package Does (One Line, Title Case)

Description Usage Arguments Value Examples

View source: R/batchHubGenerator.R

Performs all the necessary steps for the creation of an UCSC hub with all the files in a the defined folder. All the tracks saved in the path_tracks will present the same track format.

batchHubGenerator(
  path_tracks,
  pattern_tracks,
  path_local_hub,
  hub_name,
  hub_short_label,
  hub_long_label,
  email_address,
  description_url = NULL,
  assembly_database,
  gattaca_html = "http://gattaca.imppc.org/genome_browser/lplab",
  gattaca_folder_hub,
  short_label = NULL,
  long_label = NULL,
  type = NULL,
  visibility = NULL,
  color = NULL,
  autoScale = NULL,
  gattaca_user,
  gattaca_dir = "/data/apache/htdocs/genome_browser/lplab",
  quote_label = ""
)

`path_tracks`	Path with all the tracks desired in the hub. All of them will present the format defined.
`pattern_tracks`	Filtering pattern to use in the `path_tracks` for the track selection.
`path_local_hub`	Local folder of the hub where the files generated will be saved. A folder with the `hub_name` will be generated.
`hub_name`	Single-word name of the directory containing the track hub files. Not displayed to hub users.
`hub_short_label`	The short name for the track hub. Suggested maximum length is 17 characters. Displayed as the hub name on the Track Hubs page and the track group name on the browser tracks page.
`hub_long_label`	Longer descriptive label for the track hub. Suggested maximum length is 80 characters. Displayed in the description field on the Track Hubs page.
`email_address`	Email that will be provided in the hub for contact info.
`description_url`	URL to HTML page with a description of the hub's contents.
`assembly_database`	Reference genome used for alignment.
`gattaca_folder_hub`	Folder in the server where to save hub directory
`short_label`	Specifies the track's "short label", which is used in a number of places in the Browser to identify the track. For example, the short label is displayed alongside the track in the Browser image. By default the basename of the sample.
`long_label`	Specifies the track's "long label", which is also used in numerous places in the Browser to identify a track. For instance, the long label is displayed above the track's data in the Browser image. This label should be descriptive enough to allow users to uniquely identify the track within the Browser. By default the basename of the sample.
`type`	Declares the format of the data and is used to determine display methods and options. Valid settings: altGraphX, bam, bed, bed5FloatScore, bedGraph, bedRnaElements, bigBarChart, bigBed, bigInteract, bigPsl, bigChain, bigMaf, bigWig, broadPeak, chain, clonePos, coloredExon, ctgPos, downloadsOnly, encodeFiveC, expRatio, factorSource, genePred, gvf, hic, ld2, narrowPeak, netAlign, peptideMapping, psl, rmsk, snake, vcfTabix, wig, wigMaf
`visibility`	Visibility (i.e. "display mode") specifies which of 5 modes (including 'hide') should be used to display the track within the Browser image. This setting is almost always dynamically customizable by each user. The exact configuration of the display for each mode depends upon the track's type, and some modes may not be supported for certain track types. hide: DEFAULT. The track is not displayed in the Browser image unless the user changes the display setting. dense: The track is displayed as a single line or ribbon. In many cases multiple items are summarized or drawn on top of one another, and the long labels are not displayed. squish: Each item is drawn individually, but at half height and without a label. (Not supported for all types.) pack: Items are displayed individually at full height, but in a much more compact vertical space than in full mode. (Not supported for all types.) full: Each item is displayed as a separate line in the Browser image. Graphed signals may be displayed in varying heights.
`color`	Many track types allow the color of the data displayed in the image to be specified with this setting. The setting accepts red, green and blue values, each in the range of 0-255 and delimited by commas. Though this setting is widely supported, some track types in certain display modes ignore it, such as the EST tracks in dense mode. "255, 204, 153"
`autoScale`	The graph of the data displayed in the Browser image is usually scaled on the y-axis in absolute coordinates. However, you can display the data in two types of autoScale which will ensure either that the high score in the current viewing window will peak at the top of the graph, or that all tracks in a composite will be scaled according to the highest point in the viewing window of any visible tracks in the same composite. "on" or "off"
`gattaca_user`	User of gattaca server ('user@gattaca')
`gattaca_dir`	Gattaca base directory. Default=”/data/apache/htdocs/genome_browser/lplab'
`quote_label`	By defult shortLabel and longLabel are set up as the basename of the file. Is it possible to add more information using this parameter. The result long and short label will be "basename"_"quote_label". By default empty.
`track`	File to upload in the UCSC hub.

A hub folder with all the elements and tracks saved in a local host and in the server and the hub.txt to load into UCSC browser.

path <- downloadUcschubgenerator()
path_tracks <- path
pattern_tracks <- '.vcf.gz$'
hub_name <- 'example_hub_unique'
path_local_hub <- file.path(path, 'hubs')
dir.create(path_local_hub)
hub_short_label <- hub_name
hub_long_label <- 'Example of ucschubgenerator using only one type of file with a unique set of parameters'
email_address <- 'example@email.com'
assembly_database <- 'hg38'
gattaca_folder_hub <- 'exampleHub'
type <- 'vcfTabix'
visibility <- 'dense'
color <- '0, 0, 0'
gattaca_user <- 'msubirana@gattaca'
quote_label <- 'example'

batchHubGenerator(path_tracks = path_tracks,
                  pattern_tracks = pattern_tracks,
                  path_local_hub = path_local_hub,
                  hub_name = hub_name,
                  hub_short_label = hub_short_label,
                  hub_long_label = hub_long_label,
                  email_address = email_address,
                  assembly_database = assembly_database,
                  gattaca_folder_hub = gattaca_folder_hub,
                  type = type,
                  visibility = visibility,
                  color = color,
                  quote_label = quote_label,
                  gattaca_user = gattaca_user)