PhenoGram plots phenotypes that have been associated with SNPs or other locations along the genome. The genome is displayed divided into separate chromosomes as below:
Phenogram accepts a text file as the data input for generating the image. The file must be tab-delimited and recognizes the following headers. The file can contain other headers and PhenoGram will ignore them.
|POS||X||Base pair location of the SNP or in the case of a region, the starting location|
|PHENOTYPE||X||Phenotype name (required unless plotting chromosomes only)|
|END||Ending base pair location for a region|
|NOTE or ANNOTATION||Locations on the plot will be annotated to the right of the chromosomes with values from this column. The labels can be no more than 10 characters in length.|
|ETHNICITY or RACE or GROUP||Specifies the race/ethnicity for the result. When more than one occurs in the input, the plot will use different shapes to represent them.|
|COLORGROUP||Specifies a group by name and all phenotypes of the group will share a common color|
|POSCOLOR||Specified by an integer starting with 1 and lines across chromosome will have same color for same integer|
This sample file has been used to generate the examples on this site
Any text can be entered and will be displayed centered across the top of the plot.
Selects the genome to draw from the list. The genome information has been drawn from the UCSC browser for the organisms included. The input file CHR column needs to match an ID as listed in the genomes. The currently included genomes are:
A genome file can be uploaded by selecting other for genome. The genome file is a tab-delimited file and can contain the following columns. Any of the above genome files can serve as an example.
|CENTROMERE||58632012,61632012||Start,end of the centromere. If left blank, no centromere will be drawn.|
The following options control the spacing of the phenotypes along the chromosome:
The following options control the color generation of the phenotype circles on the plot:
Currently phenogram will produce images in one of the following formats:
If Cytobands is set to other, a file can be uploaded containing banding information for the genome to be plotted. The files come from the UCSC browser and the human GRCh38/hg38 cytoband file can be used as an example.
|#chrom||chr1||Chromosome number or ID.|
|chromStart||9200000||Starting base pair position for the band|
|chromEnd||12700000||Ending base pair location for the band|
|gieStain||gneg||Determines the color of the band on the plot.|