diff --git a/doc/source/web_usage.rst b/doc/source/web_usage.rst index b5c59e20a425f276c94357f37fe51441b32c0315..2986cb92aa208f47c037d8a9c071637d10d92de1 100644 --- a/doc/source/web_usage.rst +++ b/doc/source/web_usage.rst @@ -3,12 +3,167 @@ Web usage The web interface of JASS allows you to launch joint analyses over different datasets, and explore their results. -.. image:: _static/jass_welcome_page.png +The JASS software is available at the following web address: https://jass.pasteur.fr/index.html + +.. image:: _static/00__JASS_welcome_page.PNG :width: 100% :alt: JASS welcome page -The next screen lets you choose the datasets that you wish to analyse +. + +Two types of analysis are offered to the user: + 1. A genome-wide analysis (A), + 2. An analysis by region (B). + + +A - Genome-wide analysis +------------------------ +To perform a genome-wide analysis, yo have to click on the first button at the bottom of the home page of the JASS web interface (A). + +By doing so, you automatically access to the screen of the phenotypes selection that lets you choose the datasets that you wish to analyse. -.. image:: _static/jass_select_phenotypes.png +On this page, you can check the boxes corresponding to the phenotypes on which you wish to perform the genome-wide analysis. +Then, you have to validate your choice. + +If your choice is not pertinent, you receive a warning message. + +.. image:: _static/01__JASS_select_phenotypes_warning.PNG + :width: 100% + :alt: JASS phenotype selection warning page + +. + +Otherwise the analysis is started automatically. + +.. image:: _static/02__JASS_select_phenotypes.PNG :width: 100% :alt: JASS phenotype selection page + +.. image:: _static/03__JASS_select_phenotypes_progress.PNG + :width: 100% + :alt: JASS Analysis in progress page + +. + +Then, you access to the results page of the joint analysis carried out on the whole genome and on the phenotypes previously selected (A1). + +.. image:: _static/04__JASS_Manhattan_plot.PNG + :width: 100% + :alt: JASS Manhattan plot page + +. + +On this page, you can choose to export the results of your joint analysis (A1-1). + +.. image:: _static/05__JASS_data_table_export.PNG + :width: 100% + :alt: JASS data table export page + +. + +You can also choose to export all the SNP results for the phenotypes analyzed together (A1-2). + +The button is grayed out with a busy icon until the results file is available. Then the button becomes active again when the generation of results is complete. + +.. image:: _static/06__JASS_genome_full.PNG + :width: 100% + :alt: JASS genome full page + +. + +You can can also download an image in PNG format of the Manhattan plot of the jointly analyzed phenotypes (A1-3). + +.. image:: _static/07__JASS_Manhattan_download.PNG + :width: 100% + :alt: JASS Manhattan download page + +. + +You can also download an image in PNG format of the quadrant plot of the jointly analyzed phenotypes (A1-4). + +.. image:: _static/08__JASS_Quadrant_download.PNG + :width: 100% + :alt: JASS Quadrant download page + +. + +With the directlink button, you obtain an https link which allows direct access to the results of the analysis without going through the phenotype selection page (A1-5). + +This link can be copied and shared with another JASS user. + +.. image:: _static/09__JASS_direct_link.PNG + :width: 100% + :alt: JASS direct link page + +. + +Finally, you can get a table of the significant regions which you can download in CSV format (A1-6). + +.. image:: _static/10__JASS_significant_region.PNG + :width: 100% + :alt: JASS significant region page + +. + +You can also get additional information about a particular region of the genome by clicking on a point on the main Manhattan plot. + +.. image:: _static/11__JASS_zoom_Manhattan_01.PNG + :width: 100% + :alt: JASS zoom Manhattan page 01 + +.. image:: _static/12__JASS_zoom_Manhattan_02.PNG + :width: 100% + :alt: JASS zoom Manhattan page 02 + +. + +Then, you can see a heatmap of the z-scores associated with the selected phenotypes, as a function of the SNPs of the region. + +Below the heatmap, you can see a Manhattan plot zoomed in on the selected region. + +.. image:: _static/13__JASS_zoom_Manhattan_03.PNG + :width: 100% + :alt: JASS zoom Manhattan page 03 + +. + +B - Analysis by region +---------------------- +To perform an analysis by region, you have to click the second button at the bottom of the home page of the JASS web interface (B). + +By doing so, you automatically access to the selection page for the region and the phenotypes studied. + +.. image:: _static/14__JASS_LA_select_phenotypes.PNG + :width: 100% + :alt: JASS Local Analysis selection phenotypes page + +. + +On this page, you can select the chromosome number, the beginning and the end of the region (in nucleobase pairs number according to the HG37 +genome’s description). + +Like in a genome-wide analysis, you have also to select the phenotypes you wish to analyze jointly. + +Then you have to click on the button to launch the analysis by region using the chosen parameters. + +.. image:: _static/15__JASS_LA_analysis.PNG + :width: 100% + :alt: JASS Local Analysis in progress page + +. + +The results page of the analysis by region is then automatically displayed. +It provides access to the results table for the selected region, an image in PNG format of a zoom of the Manhattan plot on the genomic region studied +as well as a direct access link to the results that can be copied and shared with other users. +These functions are similar to those already presented in paragraph A and they will not be detailed again. + +On this page, two other elements are also displayed: + 1. A heatmap showing the Z-scores of the phenotypes you selected according to the positions of the SNPs expressed in number of base pairs. + 2. A zoom of the Manhattan plot on the region you selected. + +Below these two plots, you have access to a diagram showing the position of genes and exons referenced in HG37 and which ones belong +to the selected region. A color code is used to distinguish the protein coding genes, the genes rRNA from the other genes. + +.. image:: _static/16__JASS_LA_plots.PNG + :width: 100% + :alt: JASS Local Analysis plots page