d3.boxplot¶
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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)
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d3.boxplot.
change_color_theme
(theme)¶ Change color theme to the given one
Arguments: - theme (string) – theme name
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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
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d3.boxplot.
draw_axis_bckgd
()¶ Draw backgrounds of all axis
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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
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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
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d3.boxplot.
draw_legend
()¶ Draw legend
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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
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d3.boxplot.
draw_right_axis
(y_zones)¶ Draw right axis
Arguments: - y_zones (object) – name of contigs of the query
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d3.boxplot.
draw_top_axis
(x_zones:)¶ Draw top axis
Arguments: - x_zones: (object) – name of chromosomes of the target
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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
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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
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d3.boxplot.
select_query
(y)¶ Find query contig where the user click
Arguments: - y (float) – coordinate on Y axis
Returns: string|null – contig name
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d3.boxplot.
select_target
(x)¶ Find target chromosome where the user click
Arguments: - x (float) – coordinate on X axis
Returns: string|null – chromosome name
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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
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d3.boxplot.
switch_color_theme
()¶ Switch to next color theme
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d3.boxplot.
zoom_bottom_axis
()¶ Zoom on bottom axis
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d3.boxplot.
zoom_left_axis
()¶ Zoom on left axis
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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
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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
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d3.boxplot.
_get_line_len
(line)¶ Get length of a given line
Arguments: - line (array) – line object
Returns: number – line length
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d3.boxplot.
_sort_color_idy
(a, b)¶ Sort function key for color identity
Arguments: - a –
- b –
Returns: number –
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d3.boxplot.
_sort_lines
(l1, l2)¶ Sort lines with their length (DESC)
Arguments: - l1 (array) – line object
- l2 (array) – line object
Returns: number –
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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¶
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d3.boxplot.events.
init
()¶ Initialise events
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d3.boxplot.events.
filter_identity
(min_idy)¶ Remove low identity matches
Arguments: - min_idy (number) – minimum of identity. Beside it, hide matches
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d3.boxplot.events.
filter_size
(min_size)¶ Remove too small matches
Arguments: - min_size (number) – minimum size. Beside it, hide matches
Initialise context menu
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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
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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
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d3.boxplot.events.
stroke_width
(width)¶ Change matches lines stroke width
Arguments: - width (string) – new width class (“1”, “2”, or “3”)
d3.boxplot.mousetip¶
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$.fn.
mousetip
(my_tip, relative_to, x, y)¶ Mouse tip basis
Arguments: - my_tip –
- relative_to –
- x (int) –
- y (int) –
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d3.boxplot.mousetip.
init
()¶ Initialise tooltip
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d3.boxplot.mousetip.
getColorByBgColor
(bgColor)¶ Get color (black/white) depending on bgColor so it would be clearly seen.
Arguments: - bgColor –
Returns: string –
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d3.boxplot.mousetip.
get_label
(label)¶ get label to show
Arguments: - label (string) – initial label
Returns: string – new label
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d3.boxplot.mousetip.
get_match
(e)¶ Get match override by mouse cursor
Arguments: - e – mouse event
Returns: Object –
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d3.boxplot.mousetip.
hide
()¶ Hide tooltip
d3.boxplot.zoom¶
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d3.boxplot.zoom.
init
()¶ Initialize zoom.init module
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d3.boxplot.zoom.
click
()¶ Click event action
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d3.boxplot.zoom.
mousedown
()¶ Mousedown event action
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d3.boxplot.zoom.
mouseup
()¶ Mouseup event action
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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
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d3.boxplot.zoom.
restore_scale
(transform:)¶ Restore previous scale
Arguments: - transform: – transform object
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d3.boxplot.zoom.
translate
()¶ Translate event action
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d3.boxplot.zoom.
zoom
()¶ Zoom staff
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d3.boxplot.zoom.
_cursor_pos
(rect)¶ Get cursor position
Arguments: - rect (DOMRect) – if given, dont get it from DOM
Returns: