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