GwPalette Class

The GwPalette class provides constants for all color and paint types used in GW visualisations. Use these constants with the set_paint_ARBG method to customise the appearance of GW.

Background Colors

  • BACKGROUND: Main background color for the visualisation
  • BACKGROUND_TILED: Tiled background color
  • BACKGROUND_MENU: Menu background color

Primary Read Feature Colors

  • NORMAL_READ: Normal read color
  • DELETION: Deletion color
  • DUPLICATION: Duplication color
  • INVERSION_FORWARD: Forward inversion color
  • INVERSION_REVERSE: Reverse inversion color
  • TRANSLOCATION: Translocation color
  • INSERTION: Insertion color
  • SOFT_CLIP: Soft clip color

Nucleotide Colors

  • NUCLEOTIDE_A: Adenine (A) nucleotide color
  • NUCLEOTIDE_T: Thymine (T) nucleotide color
  • NUCLEOTIDE_C: Cytosine (C) nucleotide color
  • NUCLEOTIDE_G: Guanine (G) nucleotide color
  • NUCLEOTIDE_N: N (any/unknown) nucleotide color

Coverage and Track Colors

  • COVERAGE: Coverage plot color
  • TRACK: Generic data track color
  • NORMAL_READ_MQ0: Map-quality=0 normal read color
  • DELETION_MQ0: Map-quality=0 deletion color
  • DUPLICATION_MQ0: Map-quality=0 duplication color
  • INVERSION_FORWARD_MQ0: Map-quality=0 forward inversion color
  • INVERSION_REVERSE_MQ0: Map-quality=0 reverse inversion color
  • TRANSLOCATION_MQ0: Map-quality=0 translocation color
  • SOFT_CLIP_MQ0: Map-quality=0 soft clip color

BigWig and Special Features

  • BIGWIG: BigWig track display color
  • REGION_OF_INTEREST: Region of interest highlight color
  • MATE_PRIMARY: Primary mate pair color
  • MATE_SECONDARY: Secondary mate pair color
  • MATE_UNMAPPED: Unmapped mate color

Edge and Line Colors

  • SPLIT_READ: Split read edge color
  • SELECTED_ELEMENT: Selected element highlight color
  • LINE_JOINS: Line color for join connections
  • LINE_COVERAGE: Line color for coverage plots
  • LINE_LIGHT_JOINS: Light line color for join connections
  • LINE_GTF_JOINS: Line color for GTF feature joins
  • LINE_LABEL: Line color for labels
  • LINE_BRIGHT: Bright line color for emphasis

Text Colors

  • TEXT_DELETION: Text color for deletion annotations
  • TEXT_INSERTION: Text color for insertion annotations
  • TEXT_LABELS: Text color for general labels
  • TEXT_BACKGROUND: Text background color

Markers and Modifications

  • MARKERS: Color for genomic markers
  • METHYLATED_C: 5-methylcytosine (5mC) color for epigenetic modification
  • HYDROXYMETHYLATED_C: 5-hydroxymethylcytosine (5hmC) color for epigenetic modification
  • OTHER_MODIFICATION: Color for other base modifications