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 intervalschrostats
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
plot_footer_font_size
¶
type: integer
default: 10
plot_footer_font_color
¶
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 © <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
head
¶
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