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

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

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

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

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

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

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

Example with locations along chromosome and region specified:

• Input file: phenogram-mhc-sample.txt
• Title: Highlighted/li>
• Genome: human
• Phenogram spacing: Proximity
• Phenogram color: Exhaustive search
• Format: PNG
• Chromosome only?: Checked
• Chromosome: 6
• Larger font?: Checked
• Annotation?: Checked
• Transparent lines?: Checked