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Plot Parameters and Information

Plot Types

histoplot

description: The default option, used to plot histograms of the CNV frequencies per data collection ("collation") or aggregated sample data.
data_key: interval_frequencies_bundles
data_type: collations

histoheatplot

description: A "heatmap" style version of the histogram plot, where a single gain/loss frequency result is transformed into a small heat color strip.
data_key: interval_frequencies_bundles
data_type: collations

histosparkplot

description: A version of the histogram with predefined parameters for representing a small and unlabeled plot, e.g. for use in hover previews. As in the normal histogram parameters can be overridden.
data_key: interval_frequencies_bundles
data_type: collations
mods:
- plot_chro_height: 0
- plot_title_font_size: 0
- plot_area_height: 18
- plot_margins: 0
- plot_axislab_y_width: 0
- plot_grid_stroke: 0
- plot_footer_font_size: 0
- plot_width: 480
- plot_area_opacity: 0
- plot_dendrogram_width: 0
- plot_labelcol_width: 0
- plot_axis_y_max: 80
modded: histoplot

histocircleplot

description: A version circular of the histogram.
data_key: interval_frequencies_bundles
data_type: collations
mods:
- plot_width: 640
- plot_chro_height: 16
- plot_axislab_y_width: 0
- plot_area_opacity: 0
- plot_dendrogram_width: 0
- plot_labelcol_width: 0

samplesplot

description: A plot of the called CNV segments per sample, with the samples ordered by their clustering (i.e. similarity of binned CNV data).
data_key: analyses_variants_bundles
data_type: samples

geomapplot

description: A leaflet based plot of geolocations.
data_key: geolocs_list
data_type: geolocs

Plot Parameters

plot_id

default: genomeplot

plot_title

description: title above the plot

plot_group_by

description: group samples in histograms by a filter type (NCIT, PMID...)
default: ``

plot_filter_empty_samples

description: By setting to true samples w/o data can be removed e.g. from sample plots
type: boolean
default: False

force_empty_plot

description: By setting to true a plot strip will be forced even if there are no CNV samples
type: boolean
default: False

plot_cluster_results

description: By setting to false clustering can be suppressed
type: boolean
default: True

plot_samples_cluster_type

description: Selection of which measurees are used to generate the clustering matrix

  • intcoverage uses the ~2x3k (gain, loss) 1MB intervals
  • chrostats only uses the CNV coverage per chromosomal arm (separately for gains and losses)
    default: intcoverage
    oneOf: chrostats,intcoverage

plot_cluster_metric

default: ward
oneOf: average,centroid,complete,median,single,ward,weighted

plot_dup_color

default: #FFC633

plot_hldup_color

default: #FF6600

plot_del_color

default: #33A0FF

plot_hldel_color

default: #0033CC

plot_loh_color

default: #0066FF

plot_snv_color

default: #FF3300

plot_chros

type: array
items: string
default: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22

plot_width

description:

  • width of the plot image, in px
  • the plot area width is determined through
    • plot_width - 2 *plot_margins - plot_labelcol_width - plot_axislab_y_width - plot_dendrogram_width
      type: integer
      default: 1024

plot_area_height

description: height of the plot area (applies only to histogram plots)
type: integer
default: 100

plot_axis_y_max

description:

  • frequency value the maximum of the Y-axis corresponds to
  • use this to e.g. spread values if a max. of less than 100 is expected
    type: integer
    default: 100

plot_samplestrip_height

description: height of a single sample strip
type: integer
default: 12

plot_margins

description: outer plot margins, in px
type: integer
default: 25

plot_labelcol_width

description:

  • width of the space for left text labels (e.g. sample ids, collation labels)

  • defaults to 0 when only one item
    type: integer
    default: 220

plot_axislab_y_width

description: width of the space for histogram percentage markers
type: integer
default: 30

plot_dendrogram_width

description:

  • width of the cluster tree
  • defaults to 0 when no clustering is being performed
    type: integer
    default: 50

plot_dendrogram_color

description: color of the cluster tree stroke
default: #333333

plot_dendrogram_stroke

description: thickness of the cluster tree stroke
type: number
default: 0.5

plot_chro_height

description: height (well, width...) of the chromosomes in the ideogram strip
type: integer
default: 14

plot_region_gap_width

type: integer
default: 3

plot_canvas_color

description: color of the document background
default: #ffffff

plot_area_color

description: color of the plot area background
default: #eef6ff

plot_area_opacity

description: opacity of the plot background
type: number
default: 0.8

plot_heat_intensity

description: factor for frequency heatmap value brightness
type: number
default: 1

plot_grid_stroke

type: integer
default: 1

plot_grid_color

description: color of grid lines
default: #c0e3ee

plot_grid_opacity

type: float
default: 0.8

plot_font_color

default: #000000

plot_font_size

description: font size, in px
type: integer
default: 10

plot_title_font_size

description: title font size, in px
type: integer
default: 16

plot_labelcol_font_size

description: label font size (left column), in px
type: integer
default: 12

plot_label_y_font_size

description: font size for Y-axis labels (percents ...)
type: integer
default: 8

plot_label_y_font_color

description: font color for Y-axis labels (percents ...)
default: #666666

plot_label_y_values

type: array
items: integer
default: 25,50,75

plot_label_y_unit

type: string
default: %

circ_start_gap

description: in degrees; top (usually) gap providing separation & space for labels
type: integer
default: 20

circ_start_angle

description: in degrees; start of plot circle from 12 o'clock position
type: integer
default: 0

plot_probe_y_factor

description: relative y-scaling of the probes in array-/probeplots
type: integer
default: 1

plot_probe_label_y_values

type: array
items: number
default: 1,2,3,4,5,6,7,8,9

plot_probedot_size

type: integer
default: 1

plot_probedot_opacity

type: integer
default: 222

plot_region_labels

description:

  • placeholder for markers / labels in the
  • format is 8:120000000-124000000:Region+of+Interest
  • comma-concatenation for multiple values
  • label is optional
    type: array

plot_regionlabel_color

default: #ddceff

plot_gene_symbols

description:

  • label a gene's position by its symbol (CDKN2A, MYC, ERBB2...)
  • comma-concatenation for multiple values
    type: array

plot_cytoregion_labels

description:

  • label a cytoband's position (8q24, 1p12p11, 17q...)
  • comma-concatenation for multiple values
    type: array

plot_cytoregion_color

default: #ffe3ee

plot_marker_font_color

description: font color for gene and region markers
default: #dd3333

plot_marker_font_size

type: integer
default: 10

plot_marker_label_padding

description: text padding of markers versus background/box
type: integer
default: 4

plot_marker_lane_padding

type: integer
default: 2

type: integer
default: 10

default: #999999

cytoband_shades

type: object
default:
- gpos100: {'0%': 'rgb(39,39,39)', '100%': 'rgb(0,0,0)'}
- gpos75: {'0%': 'rgb(87,87,87)', '100%': 'rgb(39,39,39)'}
- gpos50: {'0%': 'rgb(196,196,196)', '100%': 'rgb(111,111,111)'}
- gpos25: {'0%': 'rgb(223,223,223)', '100%': 'rgb(196,196,196)'}
- gneg: {'0%': 'white', '100%': 'rgb(223,223,223)'}
- gvar: {'0%': 'rgb(196,196,196)', '100%': 'rgb(111,111,111)'}
- stalk: {'0%': 'rgb(39,39,39)', '100%': 'rgb(0,0,0)'}
- acen: {'0%': 'rgb(163,55,247)', '100%': 'rgb(138,43,226)'}

histoval_directions

type: object
default:
- gain_frequency: 1
- gain_hlfrequency: 1
- loss_frequency: -1
- loss_hlfrequency: -1

histoval_colorkeys

type: object
default:
- gain_frequency: plot_dup_color
- gain_hlfrequency: plot_hldup_color
- loss_frequency: plot_del_color
- loss_hlfrequency: plot_hldel_color

tiles_source

default: https://{s}.tile.openstreetmap.org/{z}/{x}/{y}.png

attribution

default: Map data &copy; <a href="https://www.openstreetmap.org/">OpenStreetMap</a> contributors, <a href="https://creativecommons.org/licenses/by-sa/2.0/">CC-BY-SA</a>

init_latitude

default: 30

init_longitude

default: 9

zoom

default: 1

default: <meta charset="utf-8"> <link rel="stylesheet" href="https://unpkg.com/leaflet@1.8.0/dist/leaflet.css" integrity="sha512-hoalWLoI8r4UszCkZ5kL8vayOGVae1oxXe/2A4AO6J9+580uKHDO3JdHb7NzwwzK5xr/Fs0W40kiNHxM9vyTtQ==" crossorigin="" />

map_w_px

default: 800

map_h_px

default: 512

marker_type

default: marker

bubble_stroke_color

default: #dd6633

bubble_stroke_weight

default: 1

bubble_fill_color

default: #cc9966

bubble_opacity

default: 0.4

marker_scale

default: 2

marker_max_r

default: 1000

zoom_min

default: 2

zoom_max

default: 14