Plot defaults

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

`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

Plot defaults

Plot Types¶

histoplot¶

histoheatplot¶

histosparkplot¶

histocircleplot¶

samplesplot¶

geomapplot¶

Plot Parameters¶

plot_id¶

plot_title¶

plot_group_by¶

plot_filter_empty_samples¶

force_empty_plot¶

plot_cluster_results¶

plot_samples_cluster_type¶

plot_cluster_metric¶

plot_dup_color¶

plot_hldup_color¶

plot_del_color¶

plot_hldel_color¶

plot_loh_color¶

plot_snv_color¶

plot_chros¶

plot_width¶

plot_area_height¶

plot_axis_y_max¶

plot_samplestrip_height¶

plot_margins¶

plot_labelcol_width¶

plot_axislab_y_width¶

plot_dendrogram_width¶

plot_dendrogram_color¶

plot_dendrogram_stroke¶

plot_chro_height¶

plot_region_gap_width¶

plot_canvas_color¶

plot_area_color¶

plot_area_opacity¶

plot_heat_intensity¶

plot_grid_stroke¶

plot_grid_color¶

plot_grid_opacity¶

plot_font_color¶

plot_font_size¶

plot_title_font_size¶

plot_labelcol_font_size¶

plot_label_y_font_size¶

plot_label_y_font_color¶

plot_label_y_values¶

plot_label_y_unit¶

circ_start_gap¶

circ_start_angle¶

plot_probe_y_factor¶

plot_probe_label_y_values¶

plot_probedot_size¶

plot_probedot_opacity¶

plot_region_labels¶

plot_regionlabel_color¶

plot_gene_symbols¶

plot_cytoregion_labels¶

plot_cytoregion_color¶

plot_marker_font_color¶

plot_marker_font_size¶

plot_marker_label_padding¶

plot_marker_lane_padding¶

plot_footer_font_size¶

plot_footer_font_color¶

cytoband_shades¶

histoval_directions¶

histoval_colorkeys¶

tiles_source¶

attribution¶

init_latitude¶

init_longitude¶

zoom¶

head¶

map_w_px¶

map_h_px¶

marker_type¶

`histoplot`¶

`histoheatplot`¶

`histosparkplot`¶

`histocircleplot`¶

`samplesplot`¶

`geomapplot`¶

`plot_id`¶

`plot_title`¶

`plot_group_by`¶

`plot_filter_empty_samples`¶

`force_empty_plot`¶

`plot_cluster_results`¶

`plot_samples_cluster_type`¶

`plot_cluster_metric`¶

`plot_dup_color`¶

`plot_hldup_color`¶

`plot_del_color`¶

`plot_hldel_color`¶

`plot_loh_color`¶

`plot_snv_color`¶

`plot_chros`¶

`plot_width`¶

`plot_area_height`¶

`plot_axis_y_max`¶

`plot_samplestrip_height`¶

`plot_margins`¶

`plot_labelcol_width`¶

`plot_axislab_y_width`¶

`plot_dendrogram_width`¶

`plot_dendrogram_color`¶

`plot_dendrogram_stroke`¶

`plot_chro_height`¶

`plot_region_gap_width`¶

`plot_canvas_color`¶

`plot_area_color`¶

`plot_area_opacity`¶

`plot_heat_intensity`¶

`plot_grid_stroke`¶

`plot_grid_color`¶

`plot_grid_opacity`¶

`plot_font_color`¶

`plot_font_size`¶

`plot_title_font_size`¶

`plot_labelcol_font_size`¶

`plot_label_y_font_size`¶

`plot_label_y_font_color`¶

`plot_label_y_values`¶

`plot_label_y_unit`¶

`circ_start_gap`¶

`circ_start_angle`¶

`plot_probe_y_factor`¶

`plot_probe_label_y_values`¶

`plot_probedot_size`¶

`plot_probedot_opacity`¶

`plot_region_labels`¶

`plot_regionlabel_color`¶

`plot_gene_symbols`¶

`plot_cytoregion_labels`¶

`plot_cytoregion_color`¶

`plot_marker_font_color`¶

`plot_marker_font_size`¶

`plot_marker_label_padding`¶

`plot_marker_lane_padding`¶

`plot_footer_font_size`¶

`plot_footer_font_color`¶

`cytoband_shades`¶

`histoval_directions`¶

`histoval_colorkeys`¶

`tiles_source`¶

`attribution`¶

`init_latitude`¶

`init_longitude`¶

`zoom`¶

`head`¶

`map_w_px`¶

`map_h_px`¶

`marker_type`¶

`bubble_stroke_color`¶

`bubble_stroke_weight`¶

`bubble_fill_color`¶