envipy's People
envipy's Issues
wie envimass temporal profiles
GUI: show ion mode for peakmaps / tables
Load calibration sample
datenatz blank / datensatz kalibration -> quantifizeriung
RT alignment mit IS
Handle multiple measurements of same experiment/sample
only consider components which can be found in all samples.
suspect screening
suspekt screening: rt egal, mehfache Treffer möglich.
Windows exe
Create exe for envipy.
Test with multiple R versions
Test on Heinz computer which libraries are loaded and which R version is found from pypeR
.
Windows Installation: which target platforms
- determine which Win platforms are requested ?
- Find instances for tests
- test.
Tests current version
- testdatensatz martin / jennifer fragen.
- matze, philipp, jenn, emma als tester
GUI overlay peakmaps
blank vs sample, sample vs sample.
simplify intstallation
Aktuelle Schritte:
- R installiert
- aktuelles „enviPat“, „enviPick“ und „nontarget“ installiert
- enviMass wie im Anhang installiert
- 64 bit Python von http://sourceforge.net/projects/winpython/files/WinPython_2.7/2.7.6.4/
(Nach Installation gibts ein WinPython Control Panel, da musst Du das noch im Menü
registrieren) - setup_envipy_0.1.1.exe (im Anhang) müsste mit den Vorgeschlagenen Einstellungen durchlaufen.
- Dann sollte im Startmenü envipy verfügbar sein.
Beim ersten Start dauert es eine Zeit, da sich das Programm erst jetzt Komponenten
herunter lädt und installiert.
Todo: Schritte 2 und 3 sparen, in dem man diese mit dem Installer ausliefert. R kann man ja Lib-Directories angeben. Da wäre es gut wenn envipy mit einem eigenen lokalen Directory arbeitet und man so sicher ist immer mit den richtigen Versionen der R-Packages zu arbeiten.
mprophet / pyprophet fuer assignment ms2 ions to precursor ion ?
Blank handling envimass
Wie werden blanks in envimass gehandhabt.
inputs: meta Daten zurodnen (Tabelle……)
Redist package only when missing
- Does Microsoft provide an official test to determine if the Redist package is missing ?
- Include this to the installer if possible.
WinPython trouble when installing to user local folder
Heinz had permission problems when installing WinPython to user local folder. Check this and find reasons.
Project bug Emma.
gal, wenn ich mein Ordner, oder irgendeine Ordner auswähle, gibt es:
C:\DATA\envipy\envipy>set SCRIPTS=C:\Users\schymaem\AppData\Roaming\envipy\Scrip
ts
C:\DATA\envipy\envipy>call C:\Users\schymaem\AppData\Roaming\envipy\Scripts\acti
vate || (call install_envipy.bat C:\DATA\envipy\WinPython-64bit-2.7.6.4\python
-2.7.6.amd64\python.exe )
Traceback (most recent call last):
File "C:\Users\schymaem\AppData\Roaming\envipy\lib\site-packages\eawag_workflo
ws-0.0.1-py2.7.egg\eawag_gui\frontend\miniwf_gui.py", line 220, in choose_projec
t
self.open_project(folder)
File "C:\Users\schymaem\AppData\Roaming\envipy\lib\site-packages\eawag_workflo
ws-0.0.1-py2.7.egg\eawag_gui\frontend\miniwf_gui.py", line 226, in open_project
self.project_model = Project(folder)
File "C:\Users\schymaem\AppData\Roaming\envipy\lib\site-packages\eawag_workflo
ws-0.0.1-py2.7.egg\eawag_gui\frontend\project.py", line 19, in init
self.create_or_load()
File "C:\Users\schymaem\AppData\Roaming\envipy\lib\site-packages\eawag_workflo
ws-0.0.1-py2.7.egg\eawag_gui\frontend\project.py", line 26, in create_or_load
self.load()
File "C:\Users\schymaem\AppData\Roaming\envipy\lib\site-packages\eawag_workflo
ws-0.0.1-py2.7.egg\eawag_gui\frontend\project.py", line 56, in load
self.load_params()
File "C:\Users\schymaem\AppData\Roaming\envipy\lib\site-packages\eawag_workflo
ws-0.0.1-py2.7.egg\eawag_gui\frontend\project.py", line 64, in load_params
with open(os.path.join(self.project_home, f_name), "r") as fp:
IOError: [Errno 2] No such file or directory: 'C:\DATA\envipy\test_project\p
eak_picker.json'
Quality plots
- envimass: calib quality plots raussuchen und erzeugen
- envimass: screening quality plots raussuchen und erzeuge
graphiken:
-
vor calib / nach calib: mass vs delta_mass (letztere mmu und ppm)
evtl mit tool top pro Punkt insbesondre ausreisser…90 % percentile als geraden parallel zur x-Achse
extra: number found IS (unique, non unique)
-
IS screening: masse (x) vs ppm(y) , fargen monoisotopisch, isotopisch
annotierung ausreisser.masse(x) vs delta rt(y) (nur monoisotopisch)
masse(x) vs intensity….mass(x), y: relative Abweichungen abundances (zuerst auf max peak normalisieren,
dann delta abundance durch abundance)mass(x) y: varianz rt isotopen intern.
Histogramm Intensitäten. und Intensität über zeit...
alles auch als extra scores in screening result Tabelle.
komponenten: Histogramm über großen der Komponenten, Varianz in rt….
- target screening genau so.
Enhancements table explorer
table explorer: filter widgets + evtl delete filtered ?
bool fields: checkbox für edit statt text.
Literature about determining mass formula from peaks.
Parameter labels envipy
- param labels aus envimass + r package doc raussuchen.
Finde IS zu gegebenen targets.
- targets: suche interne standards mit ähnlichen Namen
Test issue
test test test. did you get a notification for this issue ?
GUI: komponenten: identifizierte targets und suspscte gruppieren.
GUI: load presets from last / other project.
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