Update viewing-reports.rst

docs/source/viewing-reports.rst

@@ -1,59 +1,96 @@
 Viewing Reports
 ===============
 
-Just-DNA-Seq makes a set of reports on a genome which contain data about longevity-related gene variants, known cancer risks and drug responses.
+Just-DNA-Seq makes a set of reports on a genome which contain data about PRS, longevity-related gene variants, known cancer risks, coronary arthery disease risks and drug responses.
 
-Opening Reports
----------------
+You can learn how to get your longevity report and install Longevity Combined reporter in :doc:`getting_started`.
 
-1. Go to the **Reports** page.
+Source code on GitHub (here you also can learn how to install it from GitHub): https://github.com/dna-seq/oakvar-longevity
 
-2. In the **Longevity Combined** section, click **Download**.
 
-3. When asked by your web browser what to do with the report file, open it in the browser. The report will be opened on a new tab.
+Part 1: Polygenic risk scores (PRSs) for gaining longevity
+----------------------------------------
+
+PRS is represented as a percentile within a given population. For example, you have the 95th percentile, which means your genetic chances to gain extreme longevity is higher than 95 out of every 100 people in a chosen population.
+
+It does not take into account environmental factors and based on genetics only.
 
-4. Switch to the report tab in your browser.
+.. image:: prs.png
+  :alt: prs report
 
-Part 1: Longevity Significant Variations
+Part 2: Longevity Significant Variations
 ----------------------------------------
 
-This report contains gene variants which have significant influence on longevity. It has the following columns:
+This report contains gene variants which have significant influence on longevity. It contains the following columns:
 
-**+** - clicking this green button opens detailed information on each entry (row), and the button becomes red with a **-** sign. Clicking this **-** closes the details.
+**+** - clicking this green button opens detailed information on each entry (row), and the button becomes red with **-** sign. Clicking this **-** closed the details.
 Clicking **+** in the header opens the details for all rows and behaves in the same way (clicking **-** in the header closes all detail sections).
 
-**RSID** - the reference sequence ID of the variant.
+**RSID** - reference sequence ID of the variant.
 
 **Population** - population(s) on which the research was conducted, e.g. Greek, Ashkenazi Jewish etc., or multiple (for more details, open **+**).
 
 **Gene** - gene the variant belongs to.
 
 **Your Genotype** - which variants your genome contains. Note that in case of homozygosity two letters should be the same, and for heterozygosity they differ.
 
-**Ref allele** - the reference allele.
+**Ref allele** - reference allele.
 
-**Alt allele** - the alternative allele.
+**Alt allele** - alternative allele.
 
 **Zygosity** - hom (homozygosity) or het (heterozygosity).
 
 **Weight** - weight of this variant (the degree of significance).
 
-Part 2: Cancer Report
+.. image:: longevitymap.png
+  :alt: longevitymap report
+
+Part 3: Drugs Report
+--------------------
+
+This report contains known issues of response to certain drugs associated with gene variants. It has the following columns:
+
+**#** - number of an entry (row).
+
+**Variant/Haplotypes** - by rsID.
+
+**Drug(s)** - name(s) of drug(s) response to which is affected by the variants.
+
+**Phenotype Category**: Efficacy, Dosage, or Other.
+
+**Significance** - yes or no.
+
+**Sentence** - description of the case.
+
+**Allele Of Frequency In Cases** - allele of the variant (one or more letters A, T, C or G) in cases involved.
+
+**Allele Of Frequency In Controls** - allele of the variant in controls.
+
+**Ratio Stat Type**
+
+**Effect**
+
+Note: In some browsers the last one or two columns may be found beyond the visible area at 100% zoom level; in such cases try zooming out to 90%, 80% and so on until everything is visible.
+
+.. image:: drugs.png
+  :alt: drugs report
+
+Part 4: Cancer Report
 ---------------------
 
 This report shows variants with known cancer risks and contains the following columns:
 
 **+** - acting the same way in all reports (see above).
 
-**#** - the number of an entry (row).
+**#** - number of an entry (row).
 
 **Chrom** - chromosome the variant belongs to, e.g. **chr1**.
 
 **Position** - position of the variant on the chromosome (number).
 
 **Gene** - gene the variant belongs to, like in the previous report.
 
-**RSID** - the reference sequence ID of the variant.
+**RSID** - reference sequence ID of the variant.
 
 **cDNA Change** - change in the coding DNA by the variant.
 
@@ -65,29 +102,33 @@ This report shows variants with known cancer risks and contains the following co
 
 **Significance** - description of significance of this variant.
 
-Part 3: Drugs Report
+.. image:: cancer.png
+  :alt: cancer report
+
+Part 5: Coronary arthery disease Report
 --------------------
 
-This report contains known issues of response to certain drugs associated with gene variants. It has the following columns:
+The report shows  variants with known coronary arthery disease risks and contains the following columns:
 
-**#** - the number of an entry (row).
+**+** - acting the same way in all reports (see above).
 
-**Variant/Haplotypes** - by rsID.
+**#** - number of an entry (row).
 
-**Drug(s)** - name(s) of drug(s) response to which is affected by the variants.
+**RSID** - reference sequence ID of the variant.
 
-**Phenotype Category**: Efficacy, Dosage, or Other.
+**Gene** - gene the variant belongs to, like in the previous report.
 
-**Significance** - yes or no.
+**Risk Allele** - 
 
-**Sentence** - description of the case.
+**Genotype** - which variants your genome contains. Note that in case of homozygosity two letters should be the same, and for heterozygosity they differ.
 
-**Allele Of Frequency In Cases** - allele of the variant (one or more letters A, T, C or G) in cases involved.
+**Pubmed ID** - the ID number to access corresponding articles on PubMed
 
-**Allele Of Frequency In Controls** - allele of the variant in controls.
+**Population** - population(s) on which the research was conducted, e.g. Greek, Ashkenazi Jewish etc., or multiple (for more details, open **+**).
 
-**Ratio Stat Type** - the ratio statistics type.
+**P-Value** - 
 
-**Effect** - information on the effect.
+**Weight** - weight of this variant (the degree of significance).
 
-Note: In some browsers the last one or two columns may be found beyond the visible area at 100% zoom level; in such cases try zooming out to 90%, 80% and so on, until everything is visible.
+.. image:: coronary.png
+  :alt: Coronary arthery disease Report