Plots

To add or customise plot select "Plots" menu option.

• Use name and title input to filter the list
• Click on plot list to show the plot in the genome browser
• Click on plot list to edit the plot

Adding new plot

To add a new plot click on "Create" button and complete the form with the name, the title and the assembly of the new plot.

After clicking "Create" modified form will be displayed.

• Click "Delete" button to delete the plot
• Click "Add track" button to add new genomic track
• Click "Save" button to save modified data
• Click to show the plot in the genome browser

Adding new track

Each datasource can be displayed in browser as a separate track. To add new track to the plot click on "Add track" button.

Then choose the datasource from the select list of available datasources. You have to complete other fields of the form including:

• Title — title of the track
• No. — number of the track. Used to order tracks in the plot
• Height — height of the track. If none default size is used
• Column — colum number. Plots can have many columns

After filling the form click "Create". Then form complemented with fields specific for type of datasource (BED3, BED6, BED9, BED12, BEDGraph or Hi-C) will be shown. Detail description of each field is presented in the table below.

List of track properties

Name	Datasource type	Values	Description
Title	All	Text	Name of the track
No.	All	Integer	Track number. Used to order tracks in the plot
Height	All	Integer	Height of the track. If none default size is used
Column	All	Integer	Column number
Color	All BED, BEDGaph	Color in hex RGB without leading hash	Color of feature
Border color	All BED, BEDGraph	Color in hex RGB without leading hash	Border color of feature
Colormap	BED6, BED9, BED12, Hi-C	List of Python Matplotlib Colormaps	Colormap used to display values from 'score' column of BED datasource entry, or to display frequencies of Hi-C map
Minimum value of colormap	BED6, BED9, BED12, Hi-C	Number	Minimum value of colormap
Maximum value of colormap	BED6, BED9, BED12, Hi-C	Number	Maximum value of colormap
BEDGraph Style	BEDGraph	Line, Line with borders, Area, Area with border	Available options: Line — data will be displayed as line chart Line with borders — data will be displayed as line chart with borders Area — data will be displayed as area chart Area with border — data will be displayed as area chart with borders
BED Style	All BED	Tiles, With Introns, Flybase, Domains, Arcs	Available options: Tiles — each entry will be displayed as tile With Introns — each entry will be displayed as gene with introns (available only form BED12 fromat) Flybase — each entry will be displayed in Flybase format (available only form BED12 fromat) Domains — each entry will be displayed as triangle with one vertex lying in the middle of entry's coordinates Arcs — each entry will be displayed as semiellipse passing through coordinates of entry
Display	All BED	Stacked, Collapsed, Interlaced	Available options: Stacked — tiles will be displayed stacked Collapsed — tiles will be displayed collapsed (all shown in one line) Interlaced — tiles will be displayed interlaced (shown in two lines alternately)
Print option	All BED	Tiles, Vertical Lines, Tiles and Vertical Lines	Available options: Tiles — coordinates of entries from BED datasource will be displayed as tiles on the track Vertical Lines — coordinates of entries from BED datasource will be displayed as vertical dotted lines on all tracks of the plot Tiles and Vertical Lines — coordinates of entries from BED datasource will be displayed as tiles on the track and as as vertical dotted lines on all tracks of the plot
Labels	All BED	Yes, No	If value is set to 'Yes' labels for each feature will be printed using 'name' column value of BED
Name filter	BED6, BED9, BED12	Yes, No	If set to 'Yes' user can filter entries from BED datasource by 'name' column value
Transform	Hi-C	none, log1p, log, -log	Available options: none — values of Hi-C matrix are displayed without any transformation log1p — values of Hi-C matrix are increased by 1 and then log transformed log — values of Hi-C matrix are log transformed -log — values of Hi-C matrix are log transformed and multiplyed by -1
Domains datasource	Hi-C	List of data in BED format (public and private for user)	Coordinates of the entries from the chosen BED datasource will be used to draw domians on Hi-C track
Inverted	Hi-C	Yes, No	If set to 'Yes' Hi-C matrix will be displayed inverted

Customising plot

To customize plot click on plot list to edit the plot. Then click to customize specific track.