Merge branch 'master' of https://github.com/isb-cgc/readthedocs

docs/build/html/_sources/sections/Web-UI.txt

@@ -5,7 +5,7 @@ Documentation for the ISB-CGC web app is available from within the web-app.  Aft
 click on the down-arrow next to your name in the upper-right corner and select "Help".
 
 .. toctree::
-
+  webapp/Releases
   webapp/User-Dashboard
   webapp/Cohorts
   webapp/Visualizations

docs/build/html/_sources/sections/webapp/Cohorts.txt

@@ -3,3 +3,192 @@ Cohorts
 
 *Documentation in progress!*
 
+Cohorts are a way of creating groupings of the samples and participant data that you’re interested in looking at. You
+can create cohorts that span across multiple projects, only contain certain types of data, or focus in on a particular
+participant group.
+
+Creating and saving a cohort
+----------------------------
+**Use the create button**
+
+To create a cohort from the user dashboard, click on the “+ Create” button and select “New Cohort”. This will take you
+to the cohort creation page.
+
+**Details of new cohort page**
+
+Using the provided list of filters on the left hand side, you can select what attributes and features you are
+interested. By clicking on a feature, the field should expand and provide you with options on which to filter on. For
+example, when you click on “Vital Status”, it expands and provides a list of “Alive”, “Dead”, “None” as options to
+choose from. When you select on, the filter should appear in the Selected Filters panel and visualizations on the page
+should be updated to reflect the new cohort that has been filtered by Vital Status. The numbers beside the selectable
+filter values reflect the number of samples that have that attribute based on all other filters that have been selected.
+* Donor Filter List
+    * Project
+    * Study
+    * Vital Study
+    * Gender
+    * Age At Diagnosis
+    * Sample Type Code
+    * Tumor Tissue Site
+    * Histological Type
+    * Prior Diagnosis
+    * Pathologic State
+    * Tumor Status
+    * New Tumor Event After Initial Treatment
+    * Histological Grade
+    * Residual Tumor
+    * Tobacco Smoking History
+    * ICD-10
+    * ICD-O-3 Histology
+    * ICD-O-3 Site
+* Data Type Filter List
+    * DNA Sequencing
+    * RNA Sequencing
+    * miRNA Sequencing
+    * Protein
+    * SNP CN
+    * DNA Methylation
+
+Selected Filters Panel
+
+This is where selected filters are shown so there is an easy way to see what filters have been selected.
+Clicking on “Clear All” will remove all selected filters.
+
+Clinical Features Panel
+
+This panel shows a list of treemaps that give a high level break of the samples for a handful of features:
+* Disease Code
+* Vital Status
+* Sample Type
+* Tumor Tissue Site
+* Gender
+* Age at Initial Pathologic Diagnosis
+By using the “Show More” button, you can see two more tree maps available.
+
+Data Availability Panel
+
+This panel shows a parallel sets graph of available data for the selected samples in the cohort. The large headers over
+the vertical bars are data types. Each data type is broken up into their different platforms and “NA” for samples that
+do not have that data type. The bars that flow horizontally indicate the number of samples that have that data. By
+hovering on a horizontal segment between the first two bars, you will see the number of data that have both those data
+type platforms. You can also reorder the vertical categories by dragging the headers left and right and reorder the
+platforms by dragging the platform names up and down.
+
+**Set operations**
+
+You can create cohorts using set operations on the user dashboard page.
+
+To activate the set operations button, you must have at least one cohort selected. Upon clicking the “Set Operations”
+button, a dialogue box will appear. Here you may do the following things:
+* Enter in a name for the new cohort you’re about to create.
+* Select a set operation.
+* Edit cohorts to be used in the operation.
+
+The intersect and union operations can take any number of cohorts and in any order.
+The complement operation requires that there be a base cohort, from which the other cohorts will be subtracted from.
+Click “Okay” to complete the operation and create the new cohort.
+
+Editing a cohort
+----------------
+
+**Details of cohort edit page**
+
+Menu
+* Add New Filters: Selecting this menu item make the filters panel appear. And filters selected will be additive to any
+filters that have already been selected. To return to the previous view, you much either save any selected filters, or
+choose to cancel adding any new filters.
+* Comments: Selecting “Comments” will cause the Comments panel to appear. Here anyone who can see this cohort can
+comment on it. Comments are shared with anyone who can view this cohort and ordered by newest on the bottom.
+* Make a Copy: Making a copy will create a copy of this cohort with the same list of samples and patients and make you
+the owner of the copy.
+* Share with Others: This behaves similarly to on the user dashboard page. A dialogue box appears and the user is
+prompted to select users that are registered in the system to share the cohort with.
+
+Selected Filters Panel
+
+This panel displays any filters that have been used on the cohort or any of its ancestors. These cannot be modified and
+any additional filters applied to this cohort will be appended to the list.
+
+Details Panel
+
+This panel displays the number of samples and participant in this cohort. These vary because some participants may have
+provided multiple samples.
+This panel also displays “Your Permissions” which can be either owner or reader.
+
+Clinical Features Panel
+
+This panel shows a list of treemaps that give a high level break of the samples for a handful of features:
+* Disease Code
+* Vital Status
+* Sample Type
+* Tumor Tissue Site
+* Gender
+* Age at Initial Pathologic Diagnosis
+
+By using the “Show More” button, you can see two more tree maps available.
+
+Data Availability Panel
+
+This panel shows a parallel sets graph of available data for the selected samples in the cohort. The large headers over
+the vertical bars are data types. Each data type is broken up into their different platforms and “NA” for samples that
+do not have that data type. The bars that flow horizontally indicate the number of samples that have that data. By
+hovering on a horizontal segment between the first two bars, you will see the number of data that have both those data
+type platforms. You can also reorder the vertical categories by dragging the headers left and right and reorder the
+platforms by dragging the platform names up and down.
+
+“View File List” takes you to a new page where you can view the file list associated to the cohort you are looking at.
+The file list page provides a paginated list of files available with all samples in the cohort. Here, “available” refers
+to files that have been uploaded to the ISB-CGC Google Cloud Project and that are open access data. You can use the
+“Previous Page” and “Next Page” to show more values in the list.
+You may filter on these files if you are only interested in a specific data type and platform. Selecting a filter will
+update the list associated. The numbers next to the platform refers to the number of files available for that platform.
+There is only one menu item available and that is the “Download File List as CSV”. Selecting this item will begin a
+download process of all the files available for the cohort, taking into account the selected Platform filters. The file
+contains the following information for each file:
+* Sample Barcode
+* Platform
+* Pipeline
+* Data Level
+* File Path to the Cloud Storage Location
+
+Commenting
+Any user who owns or has had a cohort shared with them can comment on it. To open comments, use the menu button at the
+top right and select “Comments”. A sidebar will appear on the right side and any previously created comments will be
+shown.
+
+On the bottom of the comments sidebar, you can create a new comment and save it. It should appear at the bottom of the
+list of comments.
+
+Deleting a cohort
+-----------------
+
+From dashboard
+Select the cohorts that you wish to delete using the checkboxes next to the cohorts. When one or more are selected, the
+delete button will be active and you can then proceed to deleting them.
+
+From within a cohort
+If you are viewing a cohort you created, then you can delete the cohort from the top right menu option.
+
+Creating a Cohort From a visualization
+--------------------------------------
+
+To create a cohort from a visualization, you must be in plot selection mode. If you are in plot selection mode, the
+crosshairs icon in the top right corner of the plot panel should be blue. If it is not, click on it and it should turn
+blue.
+
+Once in plot selection mode, you can click and drag your cursor of the plot area to select the desired samples. For a
+cubbyhole plot, you will have to select each cubby that you are interested in.
+
+When your selection has been made, a small window should appear that contains a button labelled “Save as Cohort”. Click
+on this when you are ready to create a new cohort.
+
+Put in a name for you newly selected cohort and click the “Save” button.
+
+Copying a cohort
+----------------
+
+Copying a cohort can only be done from the cohort details page of the cohort you are want to copy.
+
+When you are looking at the cohort you wish to copy, select the “Make A Copy” item from the top right menu.
+
+This will take you to your copy of the cohort.

docs/build/html/_sources/sections/webapp/General-Permissions.txt

@@ -3,3 +3,19 @@ General Permissions
 
 *Documentation in progress!*
 
+Owner
+-----
+
+As owner of a cohort or visualization, you are able to edit and share your cohort.
+
+Reader
+------
+
+You are able to view the cohort or visualization. You may be able to make configuration changes to plots in a
+visualizations, but you will not be able to save those changes.
+
+You are able to comment on a cohort or plot and have those comments shared with everyone who can view that cohort or
+plot.
+
+In order to edit and save changes to a cohort or visualization, you will need to make a copy first. This will make you
+owner of the new copy.

docs/build/html/_sources/sections/webapp/IGV-Browser.txt

@@ -3,3 +3,13 @@ IGV-Browser
 
 *Documentation in progress!*
 
+The IGV Browser connects to the Google Genomics API. The ISB-CGC Project has both open and protected datasets. If you
+are authorized to access protected access datasets, they will appear in the selection options. You must select a dataset,
+which will display the related readgroupsets. You can select one or more readgroupsets to display.
+
+Accessing the IGV Browser
+-------------------------
+
+To access the IGV browser, go to the cohort file list page. The file listing table includes a column labelled “IGV”. For
+those files that also have a ReadGroupSet ID in Google Genomics, a green check mark will appear in the column. Clicking
+on that link will take you to the IGV browser with the appropriate dataset and readgroupset preselected.

docs/build/html/_sources/sections/webapp/SeqPeek.txt

@@ -3,3 +3,41 @@ SeqPeek
 
 *Documentation in progress!*
 
+SeqPeek is a visualization designed to show mutations on a protein associated to a Gene. It allows users to select
+multiple cohort and view mutations on a single gene across all of those cohorts.
+
+Creating a SeqPeek Visualization
+--------------------------------
+
+You can create a new SeqPeek visualization from the user dashboard. Select the “SeqPeek” option from the “+ Create”
+menu. This will automatically take you to a SeqPeek page with no settings preselected for you. To make changes, open
+the Settings panel.
+
+In the Settings panel, there will be options to select in order to make a new plot.
+* Gene selection: This is an autocompleting dropdown that will search the database for valid genes the system has data
+for.
+* Cohorts: This is where you can select one or more cohorts to plot at one time.
+
+To add a cohort, select the “+ Cohort” option underneath the currently selected list of cohorts. This will take you to
+the cohorts listing panel where you can select a cohort from the list, or use the autocomplete textbox to search in
+their list of cohorts.
+When all the settings have been set, you can click “Update Plot” to regenerate the plot with the new settings.
+
+Saving a SeqPeek Visualization
+------------------------------
+
+To save changes to the visualization, click “Save Visualization” button. This will prompt you to name your SeqPeek
+visualization and save. You will be notified if it saved correctly or not.
+
+
+Deleting a SeqPeek Visualization
+--------------------------------
+
+**From User Dashboard**
+
+Select the SeqPeek visualizations that you wish to delete using the checkboxes next to the visualization. When one or
+more are selected, the delete button will be active and you can then proceed to deleting them.
+
+**From SeqPeek Visualization**
+
+If you are viewing a SeqPeek visualization you created, then you can delete the cohort from the top right menu option.

docs/build/html/_sources/sections/webapp/Sharing.txt

@@ -3,3 +3,31 @@ Sharing
 
 *Documentation in progress!*
 
+Sharing a cohort
+----------------
+
+A cohort can only be shared by the owner of the cohort.
+
+The person the cohort is shared with has read only access. If they would like to be able to edit the cohort, they would
+first need to make a copy of it. This only copies the list of samples and participants associated to the cohort, and not
+any additional information that is private to the original owner of the cohort.
+
+Sharing a visualization
+-----------------------
+
+A visualization can only be shared by the owner of the visualization.
+
+The person the visualization is shared with has read only access. They may make changes to the plot settings, but they
+will not be able to save those changes. If they want to be able to save changes, they need to clone the visualization
+first. Underlying cohorts are shared with the user when the visualization is shared.making changes to those cohorts will
+require the user to first clone the cohort as noted above.
+
+Sharing a SeqPeek visualization
+-------------------------------
+
+A SeqPeek visualization can only be shared by the owner of the visualization.
+
+The person the SeqPeek visualization is shared with has read only access. They may make changes to the settings, but
+they will not be able to save those changes. If they want to be able to save changes, they need to clone the SeqPeek
+visualization first. Underlying cohorts are shared with the user when the visualization is shared.making changes to
+those cohorts will require the user to first clone the cohort as noted above.