Phenogram examples

Phenogram created the image below using the sample file provided. The settings used:

  • Input file: phenogram-sample.txt
  • Title: Sample
  • Genome: human
  • Phenogram spacing: Proximity
  • Phenogram color: Exhaustive search
  • Format: PNG
  • Cytobands: human

Pheno-gram-sample

Example showing mouse genome and cytogenetic bands:

  • Input file: phenogram-sample-mouse.txt
  • Title: Sample Mouse
  • Genome: mouse
  • Phenogram spacing: Proximity
  • Phenogram color: Exhaustive search
  • Format: PNG
  • Cytobands: mouse

Pheno-gram-mouse

Example showing chromosome 1 only and cytogenetic bands:

  • Input file: phenogram-sample.txt
  • Title: Sample Chromosome 1 Only
  • Genome: human
  • Phenogram spacing: Proximity
  • Phenogram color: Exhaustive search
  • Format: PNG
  • Chromosome: 1
  • Larger font?: Checked
  • Cytobands: human
  • Phenotype size: large

Pheno-gram-zoom-sample

Example showing chromosomes 1,4,7X only and cytogenetic bands:

  • Input file: phenogram-sample-mouse.txt
  • Title: Sample Mouse Chromosomes 1,4,7,X
  • Genome: mouse
  • Phenogram spacing: Proximity
  • Phenogram color: Exhaustive search
  • Format: PNG
  • Chromosome: 1,4,7,X
  • Cytobands: mouse

Pheno-gram-specified-chroms

Example using phenotypes grouped (with COLORGROUP column) for display:

  • Input file: phenogram-groups-sample.txt
  • Title: Phenotypes Grouped by Color
  • Genome: human
  • Phenogram spacing: Proximity
  • Phenogram color: Grouped colors
  • Format: PNG
  • Outline circles?: Checked

Pheno-gram-groups-sample

Example with ANNOTATION and ETHNICITY columns:

  • Input file: phenogram-ancestry-sample.txt
  • Title: Annotation and ancestry
  • Genome: human
  • Phenogram spacing: Proximity
  • Phenogram color: Exhaustive search
  • Format: PNG
  • Larger font?: Checked
  • Annotation?: Checked
  • Outline circles?: Checked

Phenogram-ancestry-annotation

Example with locations along chromosome with regions highlighted

  • Input file: phenogram-sample-poscolor.txt
  • Title: Base pair locations and highlighted region
  • Genome: human
  • Phenogram spacing: Proximity
  • Phenogram color: Exhaustive search
  • Format: PNG
  • Chromosome only?: Checked
  • Transparent lines?: Checked

Phenogram-redblue-sample

Example with locations along chromosome and region specified:

  • Input file: phenogram-chrom-only-sample.txt
  • Title: Base pair locations and highlighted region
  • Genome: human
  • Phenogram spacing: Proximity
  • Phenogram color: Exhaustive search
  • Format: PNG
  • Chromosome only?: Checked
  • Larger font?: Checked
  • Annotation?: Checked
  • Transparent lines?: Checked

Phenogram-lines-region-sample