Create Manhattan Plot for GWAS (Genome-Wide Association Studies).

• Purpose
  This app can be used to create Manhattan Plot for GWAS.
  Features include:
  1. Customize chromosome label.
  2. Option to use log of P-value.
  3. Specify color to alternate for different chromosomes.
  4. Specify customized color for highlighting the special SNP (Single Nucleotide Polymorphism, rs number).
  5. Customize suggestive line settings.
  6. Customize genome-wide line settings.

• Installation
  Download the file Manhattan Plot for GWAS.opx, and then drag-and-drop onto the Origin workspace. An icon will appear in the Apps Gallery window.
• Operation
  1. Import desired data into a worksheet.
  2. With worksheet active, click the icon in the Apps Gallery window.
  3. In the pop up dialog, select the desired columns for the related inputs.
  4. Change the settings of suggestive line and genome-wide line as needed.
  5. Click OK button to create manhattan plot for GWAS.

• Dialog Settings
  • Chromosome (CHR): Data for chromosome number. Basically, the values are from 1 to 22, plus X (23), Y (24), and MT (25), etc.
  • Chromosome Label: The label used for the chromosome axis (X axis). If not specified, the label will be from CHR data.
  • Genomic Coordinate (BP): Data for genomic coordinate (chromosomal position).
  • P-Value (P): Data for P-value.
  • Use -Log10(P): If checked, the -log10(P) is used for the plot, other wise, the raw P-value is used.
  • Color to Alternate: If specified, the colors are alternated for chromosome according to the specified color indices.
  • SNP: Specify data for single nucleotide polymorphism (rs number).
  • Highlight SNP: Specify data for SNP to highlight, the highlight SNP needs to be subset of SNP.
  • Highlight Color: The color for the highlighted SNP.
  • Suggestive Line: Specify whether to show the suggestive line, Y value of the line and its color.
  • Genome-Wide Line: Specify whether to show the genome-wide line, Y value of the line and its color.