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
![](/assets/pheno-gram-sample-44ec64bb305d255eb7f5ceceb6aff643341ddf280c54b3cbac35e78ecc3e4da5.png)
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
![](/assets/pheno-gram-mouse-d121bf816d20ccd1e3388372c1110b9295a4c318776ab77281d9614ee6074b75.png)
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
![](/assets/pheno-gram-zoom-sample-d528cf0dc4a16c40155dfeddeb9e6d399cc09f071f081069da30488f29917d25.png)
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
![](/assets/pheno-gram-specified-chroms-06e0ec2cdc945fa067cbf6d4e14914ffe23c9d7fe49d905b77a61153ad0c37cd.png)
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
![](/assets/pheno-gram-groups-sample-3c1048120d65d341e789e76f739f6706014a0b804472f0894f8d8f0ac0f97b3a.png)
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
![](/assets/phenogram-ancestry-annotation-e9207de8bf3cbadb69104fc6ae829c087a92b9f2d0cc59e501bf44c910d64eeb.png)
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
![](/assets/phenogram-redblue-sample-b13b2960c275349861e1cea17e7a50cc1847b01504251e8417162d6fad748020.png)
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
![](/assets/phenogram-lines-region-sample-a17d18bb068990ca871dfc6f9e602ea81e184ec549f48c5bef1b44183f0a53d9.png)