d3.boxplot

d3.boxplot.init(id_res, from_file)

Initialize dotplot

Arguments:
  • id_res (string) – job id
  • from_file (boolean) – true to load data from a file (default: false, load from server)
d3.boxplot.change_color_theme(theme)

Change color theme to the given one

Arguments:
  • theme (string) – theme name
d3.boxplot.draw(x_contigs, x_order, y_contigs, y_order)

Draw dot plot

Arguments:
  • x_contigs (object) – length associated to each contig of the query
  • x_order (array) – order of query contigs
  • y_contigs (object) – length associated to each chromosome of the target
  • y_order (array) – order of target chromosomes
d3.boxplot.draw_axis_bckgd()

Draw backgrounds of all axis

d3.boxplot.draw_bottom_axis(x_max, x_min)

Draw bottom axis

Arguments:
  • x_max (int) – max value of x on the X axis
  • x_min (int) – min value of x on the X axis
d3.boxplot.draw_left_axis(y_max, y_min)

Draw left axis

Arguments:
  • y_max (int) – max value of y on the Y axis
  • y_min (int) – min value of y on the Y axis
d3.boxplot.draw_legend()

Draw legend

d3.boxplot.draw_lines(lines, x_len, y_len)

Draw matches on dot plot

Arguments:
  • lines (object) – matches definition
  • x_len (number) – total len of target
  • y_len (number) – total len of query
d3.boxplot.draw_right_axis(y_zones)

Draw right axis

Arguments:
  • y_zones (object) – name of contigs of the query
d3.boxplot.draw_top_axis(x_zones:)

Draw top axis

Arguments:
  • x_zones: (object) – name of chromosomes of the target
d3.boxplot.get_human_readable_size(nbases, precision, space)

Get human readable size in Kb or Mb for a number in bases

Arguments:
  • nbases (int) – size in bases
  • precision (int) – unit to use (auto: select according to number size)
  • space (string) – space before unit (space or non-breaking space for example)
Returns:

string – human readable size

d3.boxplot.launch(res, update, noise_change)

Launch draw of dot plot

Arguments:
  • res (string) –
  • update (boolean) – if true, just update the existing dot plot (don’t initialize events)
  • noise_change (boolean) – if false, set noise to true
d3.boxplot.select_query(y)

Find query contig where the user click

Arguments:
  • y (float) – coordinate on Y axis
Returns:

string|null – contig name

d3.boxplot.select_target(x)

Find target chromosome where the user click

Arguments:
  • x (float) – coordinate on X axis
Returns:

string|null – chromosome name

d3.boxplot.select_zone(x, y, x_zone, y_zone, force)

Find zone (query contig and target chromosome) based on coordinates

Arguments:
  • x (float) – coordinate on X axis
  • y (float) – coordinate on Y axis
  • x_zone (string) – selected chromosome on X axis (target)
  • y_zone (string) – selected contig on Y axis (query)
  • force (boolean) – if true, select zone even if a zone is already selected
d3.boxplot.switch_color_theme()

Switch to next color theme

d3.boxplot.zoom_bottom_axis()

Zoom on bottom axis

d3.boxplot.zoom_left_axis()

Zoom on left axis

d3.boxplot.__draw_idy_lines(idy, lines, x_len, y_len)

Draw matches on dot plot for the given identity class

Arguments:
  • idy (string) – identity class of matches to draw
  • lines (object) – matches definitions
  • x_len (number) – total length of target
  • y_len (number) – total length of query
d3.boxplot.__lineFunction(d, min_size, max_size, x_len, y_len)

Build line data for D3.js

Arguments:
  • d (object) – data object of the line
  • min_size (int) – min size of line. Beside it, don’t draw the line
  • max_size (int|null) – max size of line. Over it, don’t draw the line
  • x_len (number) – length of x (target)
  • y_len (number) – length of y (query)
Returns:

string – path object

d3.boxplot._get_line_len(line)

Get length of a given line

Arguments:
  • line (array) – line object
Returns:

number – line length

d3.boxplot._sort_color_idy(a, b)

Sort function key for color identity

Arguments:
  • a
  • b
Returns:

number

d3.boxplot._sort_lines(l1, l2)

Sort lines with their length (DESC)

Arguments:
  • l1 (array) – line object
  • l2 (array) – line object
Returns:

number

d3.boxplot._sort_lines_by_idy(l1, l2)

Sort lines with their identity (DESC)

Arguments:
  • l1 (array) – line object
  • l2 (array) – line object
Returns:

number

d3.boxplot.events

d3.boxplot.events.init()

Initialise events

d3.boxplot.events.filter_identity(min_idy)

Remove low identity matches

Arguments:
  • min_idy (number) – minimum of identity. Beside it, hide matches
d3.boxplot.events.filter_size(min_size)

Remove too small matches

Arguments:
  • min_size (number) – minimum size. Beside it, hide matches
d3.boxplot.events.init_context_menu()

Initialise context menu

d3.boxplot.events.set_break_lines_visibility(value:)

Set break lines visibility: color and thickness, or hidden

Arguments:
  • value: (string) – visibility value: “0”-> hidden to “5” -> max visibility value
d3.boxplot.events.stroke_linecap(rounded)

If stroke precision checked, strole-linecap is set to “butt”. Else “round” to improve visibility of matches

Arguments:
  • rounded (boolean) – if true, improve bisibility by add round cap to lines
d3.boxplot.events.stroke_width(width)

Change matches lines stroke width

Arguments:
  • width (string) – new width class (“1”, “2”, or “3”)

d3.boxplot.mousetip

$.fn.mousetip(my_tip, relative_to, x, y)

Mouse tip basis

Arguments:
  • my_tip
  • relative_to
  • x (int) –
  • y (int) –
d3.boxplot.mousetip.init()

Initialise tooltip

d3.boxplot.mousetip.getColorByBgColor(bgColor)

Get color (black/white) depending on bgColor so it would be clearly seen.

Arguments:
  • bgColor
Returns:

string

d3.boxplot.mousetip.get_label(label)

get label to show

Arguments:
  • label (string) – initial label
Returns:

string – new label

d3.boxplot.mousetip.get_match(e)

Get match override by mouse cursor

Arguments:
  • e – mouse event
Returns:

Object

d3.boxplot.mousetip.hide()

Hide tooltip

d3.boxplot.zoom

d3.boxplot.zoom.init()

Initialize zoom.init module

d3.boxplot.zoom.click()

Click event action

d3.boxplot.zoom.mousedown()

Mousedown event action

d3.boxplot.zoom.mouseup()

Mouseup event action

d3.boxplot.zoom.reset_scale(temp, after, force)

Reset scale

Arguments:
  • temp (boolean) – if true, reset it temporarily
  • after (function) – function to launch after staff
  • force (boolean) – do it even if events are disabled
Returns:

boolean – true if done, else false

d3.boxplot.zoom.restore_scale(transform:)

Restore previous scale

Arguments:
  • transform: – transform object
d3.boxplot.zoom.translate()

Translate event action

d3.boxplot.zoom.zoom()

Zoom staff

d3.boxplot.zoom._cursor_pos(rect)

Get cursor position

Arguments:
  • rect (DOMRect) – if given, dont get it from DOM
Returns: