-
Notifications
You must be signed in to change notification settings - Fork 40
Unwritten Documentation Requirements
This page contains a list of topics which require help files, but those help files have not yet been written. If you're seeking help using MicrobeTrace, please see visit the Help Portal.
If the above warning hasn't dissuaded you and you read this document, and see a bullet point which you believe covers your use case, please review the existing open issues to see if someone else already shares your concern, and comment on the relevant issue if that is the case. If not, please submit a new issue.
content of input file screen including status messages, progress bar.
- description of input checking, error and information dialog boxes - i.e. might go wrong with csv and fasta inputs
- description of various column types and how they are used for node/edge annotation (categorical, numeric, has_nulls)
- how to color nodes and edges
- how to filter edges by threshold slider
- how to display maps, spreadsheet, histograms
- how to cross select nodes from one display to another
- how to zoom in and out, how to change all display parameters via menu
- how to single select, multiple select, single deselect nodes
- how to change displayed edges via threshold
- (nodes connected by nodes with length less than threshold length)
- content of spreadsheet
- only rows from node csv with names matching fasta and output from hivtrace are kept
- only rows from node csv with names matching edge csv are kept
- describe all gui elements of spreadsheet - how to filter, sort, set row display limit
- how to singly select and deselect nodes, how to multiply select nodes
- content of map
Node and edge attributes can be mapped to elements of the interactive graphic. Specifically, categorical variables can be mapped to color and shape characteristics whereas continuous variables are mapped to size and transparency/opacity. String attributes, such as geographic region, can also be displayed as textual labels anchored to its parent element. For example, a two-letter State code can be superimposed on a node.
- only rows from node csv with both lat, long columns and non-null entries
- how to single select, multiple select, and single deselect nodes
- content of histogram HIV-sequence data is input and processed into a comma-separated ?edge list? (Fig2). The edge list represents the cumulative distribution of genetic distances between HIV sequences.
This distribution can be visualized as a histogram.
- what is it exactly
- how should it inform the threshold setting
- how to select nodes to be included in histogram
Everything about it.
- What it is good for (Viewing Sequence Alignments)
- Some of its advanced features (e.g. FASTA Exporting, Newick Rendering)
What can go wrong will go wrong. How to tell what went wrong and how to fix it.
- flow chart with debug/correction steps
- list of pre-checked debug input files and what output from them should look like
- how to find status data to attach to debug request email
- how to do screen dumps to attach to debug request email
- email of CDC support rep
- how to bring up javascript debug window during support call
- list of debug commands and expected results
Copyright 2017-2018 Centers for Disease Control and Prevention • Acknowledgements