https://github.com/morganconrad/fcs
Javascript / node.js code to read FCS flow cytometry data
https://github.com/morganconrad/fcs
fcs flow-cytometry javascript nodejs
Last synced: about 1 year ago
JSON representation
Javascript / node.js code to read FCS flow cytometry data
- Host: GitHub
- URL: https://github.com/morganconrad/fcs
- Owner: MorganConrad
- License: mit
- Created: 2013-11-09T21:32:11.000Z (over 12 years ago)
- Default Branch: master
- Last Pushed: 2023-06-19T22:22:23.000Z (almost 3 years ago)
- Last Synced: 2024-04-26T09:41:24.469Z (about 2 years ago)
- Topics: fcs, flow-cytometry, javascript, nodejs
- Language: JavaScript
- Size: 842 KB
- Stars: 17
- Watchers: 6
- Forks: 10
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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# fcs
Javascript / node.js code to read FCS flow cytometry data. Will read all of the HEADER, TEXT, and ANALYSIS segments into key/value pairs. Reads raw (likely uncompensated) data as well, either into numeric arrays for further analysis, or as Strings for quickly scanning the data.
## basic usage
1. Get the FCS file into a Buffer
2. Create a new FCS(theBuffer, options)
e.g. to read from a file asynchronously
```javascript
var FCS = require('fcs');
FS.readFile(filename, function(err, databuf) {
if (err) {
console.error(err);
}
else {
var fcs = new FCS(options, databuf);
// do something with fcs
}
});
```
### see fcscli.js or fcshttp.js in the examples folder for usage examples
## options (default in bold)
* dataFormat: 'asNumber', '**asString**', 'asBoth', or 'asNone'
* groupBy: '**byEvent**', 'byParameter'
* decimalsToPrint: **2**
* eventsToRead: **1000** // an integer, -1 means "all events"
* maxPerLine: **10**
* eventSkip: **0** if eventsToRead is less than the events in the file, this allows you to more randomly sample. A value of 'true' has them equally distributed. 0 means read the first events from the file.
Any additional options are ignored, but will be printed under a "meta" segment in the JSON. For example, you might want to include a date, your laboratory, etc...
# api
## creational
### var myFCS = new FCS(options, buffer)
Constructor. Both arguments are optional.
If buffer is present it will be read, otherwise you need to call **readBuffer()** or **readStreamAsync()** later
### myFCS.options(options)
Set or add options.
### myFCS.readBuffer(buffer, moreOptions)
Read data from buffer. moreOptions are optional. Hopefully by now you've set them all! :-)
### myFCS.readStreamAsync(readStream, moreOptions, callback)
Reads data asynchronously from a readStream. moreOptions is optional. When complete, calls `callback(err, fcs)`.
### myFCS.prepareWriteableStream(callback, readableStream)
The readableStream arg is optional. Creates a writeableStream ready to parse an FCS format file. e.g.
var fws = fcs.prepareWriteableStream(callback, readableStream);
readableStream.pipe(fws);
When piping is complete, will call `callback(err, fcs)`.
## retrieving the data
### get(segment, keywords...)
segment should be one of ('text', 'analysis', or, more rarely, 'header', 'meta').
If no keywords are provided, returns that entire segment
otherwise, returns a single value, stopping at the first match to the keyword.
Returns null if none were found.
### getText(keywords...)
Equivalent to get('text', keywords)
*e.g.* `text('$P3N') might return 'FL1-H'
### get$PnX(x)
Return an array of all N keywords for that P.X combination. The 0th value will be empty.
*e.g.* `get$PnX('N') might return ['', 'FSC, 'SSC', 'FL1-H', ...]
### getAnalysis(keyword, additionalKeywords...)
Equivalent to get('analysis', keywords)
### getNumericData(oneBasedIndex)
Returns an array of Numbers for the respective event or parameter, iff you requested numeric data.
### getStringData(oneBasedIndex)
Returns an array of Strings for the respective event or parameter, iff you requested string data.
### getOnly(onlys)
Returns a subset of the JSON, based upon onlys, an array of dot delimited Strings
*e.g.* getOnlys(['meta','text.$P1N') would return all of meta, plus parameter 1 name
## fields
### .header
Holds the HEADER segment (first 256 bytes). The version is header.FCSVersion
### .text
Holds all the TEXT segment
### .analysis
Holds all the ANALYSIS segment. If none, is an empty object {}
### .meta
Holds all the options, plus a bit more
## Todos and Gotchas [official bugs here](https://github.com/MorganConrad/fcs/issues)
- doesn't handle $BEGINSTEXT, $ENDSTEXT
- could do more with Millipore's XML ANALYSIS
## Changelog
- v0.1.0 17 Nov 2018 partly converted to use ES6 features