produce pdf - Githubissues

AlixDahirel commented 12 years ago

Hi, Sorry to bother you but I cant find the produce pdf button in CytoSpade... Many thanks for your help!

Alix

zbjornson commented 12 years ago

Hi Alix, please see here: http://utopia.stanford.edu/pdfs.jpg -Zach

AlixDahirel commented 12 years ago

Got it. Thanks!

Alix Scholer-Dahirel, PhD Research Project Manager, U830/U932 Institut Curie 26 rue d'Ulm 75005 Paris, France Tel: +33 (0)1 56 24 58 05

De : Zach Bjornson [notifications@github.com] Date d'envoi : vendredi 28 septembre 2012 16:15 À : nolanlab/spade Cc : Dahirel Alix Objet : Re: [spade] produce pdf (#48)

Hi Alix, please see here: http://utopia.stanford.edu/pdfs.jpg -Zach

— Reply to this email directly or view it on GitHubhttps://github.com/nolanlab/spade/issues/48#issuecomment-8977598.

zbjornson commented 12 years ago

Great. Additionally -- I think I've fixed the plugin so that you don't have to worry about the period/comma issue anymore. However, I haven't been able to test it thoroughly because I don't have a machine with a foreign-language OS. If you want to try it, please follow these steps:

Download this file: https://github.com/nolanlab/spade/raw/master/inst/tools/CytoSPADE.jar
Put that file in your Cytoscape plugins directory. This is probably C:\Program Files\Cytoscape_v2.8.3\plugins for you. Click "ok" or "replace" to acknowledge that you're replacing the existing file with the same name.
Restart Cytoscape and run the wizard again. In the final screen when it shows a large white text box with your selected parameters, the flowcore::arcsinhTransform(...) line should have a decimal instead of a comma now.

Let me know if it works if your try it, please.

Thanks! Zach

AlixDahirel commented 12 years ago

Hi,

I tried that but I still see a period in the final screen. In addition, I get an error message:

R est un logiciel libre livr'e sans AUCUNE GARANTIE. Vous pouvez le redistribuer sous certaines conditions. Tapez 'license()' ou 'licence()' pour plus de d'etails.

R est un projet collaboratif avec de nombreux contributeurs. Tapez 'contributors()' pour plus d'information et 'citation()' pour la facon de le citer dans les publications.

Tapez 'demo()' pour des d'emonstrations, 'help()' pour l'aide en ligne ou 'help.start()' pour obtenir l'aide au format HTML. Tapez 'q()' pour quitter R.

!/usr/bin/env Rscript

^^set this to your Rscript path

#

runSPADE: R wrapper script for SPADE tree construction

Erin Simonds - esimonds@stanford.edu

Version 2.5 - June 29, 2012

Autogenerated by CytoSPADE

#

Command line instructions:

1) Make sure the first line of this file is your Rscript path (found in the same directory as R)

#

2) Move the entire directory containing this script and the FCS file(s) to be analyzed to the computer on which you will run SPADE

#

3) In a command shell, navigate to the folder containing this script and the FCS file(s) to be analyzed

#

4) Make this script executable. At the command line, run:

$ chmod +x runSPADE.R

#

5a) For normal use (not in a load sharing or compute cluster): At the command line, run:

$ ./runSPADE.R [-num_threads=X] [-file_to_process=Y]

where X is the number of threads you wish to use (default = 1)

Y is the name of the file to process (default = use file(s) specified in this script)

Note that parameters in brackets may be omitted.

#

5b) For Sun Gridengine: At the command line, run:

$ qsub -cwd -j y -b y -m e -M username@domain.ext [-pe threaded A] ./runSPADE.R [-num_threads=X] [-file_to_process=Y]

where username@domain.ext is your e-mail address to e-mail when the job is done,

A is the number of slots to reserve with Gridengine,

X is the number of threads to use in SPADE (usually the same as A) (default = 1).

Y is the name of the file to process (default = use file(s) specified in this script)

Note that parameters in brackets may be omitted.

#

5c) For Platform LSF: At the command line, run:

$ bsub [-n A -R "span[hosts=1]"] ./runSPADE.R [-num_threads=X] [-file_to_process=Y]

A is the number of slots to reserve with LSF,

X is the number of threads to use in SPADE (usually the same as A) (default = 1).

Y is the name of the file to process (default = use file(s) specified in this script)

Note that parameters in brackets may be omitted. (Note that the brackets surrounding "hosts=1" do not indicate an optional parameter.)

#

Interactive instructions:

1) Move the entire directory containing this script and the FCS file(s) to be analyzed to the computer on which you will run SPADE

2) In an interactive R session, change the working directory to the folder created in step 1

3) At the R command line, run: source("runSPADE.R")

#

BEGIN AUTOGENERATED DATA

FILE_TO_PROCESS="." CLUSTERING_MARKERS=c("DAPI-A","FITC-A") PANELS=list(

list(

panel_files=c("574 309 1 Cristina110704_574 309 T.fcs"),

median_cols=NULL,

reference_files=NULL,

fold_cols=NULL

)) TRANSFORMS=flowCore::arcsinhTransform(a=0, b=0.2) Scalable Robust Estimators with High Breakdown Point (version 1.3-02)

DOWNSAMPLED_EVENTS=5000 DOWNSAMPLING_TARGET_PCTILE=NULL TARGET_CLUSTERS=200 CLUSTERING_SAMPLES=50000 DOWNSAMPLING_EXCLUDE_PCTILE=0.01 NODE_SIZE_SCALE_FACTOR=1.2 NORMALIZE="global" OUTPUT_DIR="output/"

END AUTOGENERATED DATA

LIBRARY_PATH=NULL NUM_THREADS <- 1 for (e in commandArgs()) {

ta <- strsplit(e,"=",fixed=TRUE)

if( ta[[1]][1] == "-num_threads") {

NUM_THREADS <- ta[[1]][2]

}

if( ta[[1]][1] == "-file_to_process") {

FILE_TO_PROCESS <- ta[[1]][2]

}

} Sys.setenv("OMP_NUM_THREADS"=NUM_THREADS) library("spade",lib.loc=LIBRARY_PATH) Le chargement a n'ecessit'e le package : igraph LAYOUT_FUNCTION=layout.kamada.kawai SPADE.driver(FILE_TO_PROCESS, filepattern=".fcs", out_dir=OUTPUT_DIR, cluster_cols=CLUSTERING_MARKERS, panels=PANELS, transforms=TRANSFORMS, layout=LAYOUT_FUNCTION, downsampling_samples=DOWNSAMPLED_EVENTS, downsampling_target_pctile=DOWNSAMPLING_TARGET_PCTILE, downsampling_exclude_pctile=DOWNSAMPLING_EXCLUDE_PCTILE, k=TARGET_CLUSTERS, clustering_samples=CLUSTERING_SAMPLES) Erreur dans SPADE.driver(FILE_TO_PROCESS, filepattern = ".fcs", out_dir = OUTPUT_DIR, : argument(s) inutilis'e(s) (transforms = TRANSFORMS) Ex'ecution arr^et'ee

Alix Scholer-Dahirel, PhD Research Project Manager, U830/U932 Institut Curie 26 rue d'Ulm 75005 Paris, France Tel: +33 (0)1 56 24 58 05

De : Zach Bjornson [notifications@github.com] Date d'envoi : vendredi 28 septembre 2012 16:21 À : nolanlab/spade Cc : Dahirel Alix Objet : Re: [spade] produce pdf (#48)

Great. Additionally -- I think I've fixed the plugin so that you don't have to worry about the period/comma issue anymore. However, I haven't been able to test it thoroughly because I don't have a machine with a foreign-language OS. If you want to try it, please follow these steps:

Download this file: https://github.com/nolanlab/spade/raw/master/inst/tools/CytoSPADE.jar
Put that file in your Cytoscape plugins directory. This is probably C:\Program Files\Cytoscape_v2.8.3\plugins for you. Click "ok" or "replace" to acknowledge that you're replacing the existing file with the same name.
Restart Cytoscape and run the wizard again. In the final screen when it shows a large white text box with your selected parameters, the flowcore::arcsinhTransform(...) line should have a decimal instead of a comma now.

Let me know if it works if your try it, please.

Thanks! Zach

— Reply to this email directly or view it on GitHubhttps://github.com/nolanlab/spade/issues/48#issuecomment-8977799.

nolanlab / spade

produce pdf #48

!/usr/bin/env Rscript

^^set this to your Rscript path

runSPADE: R wrapper script for SPADE tree construction

Erin Simonds - esimonds@stanford.edu

Version 2.5 - June 29, 2012

Autogenerated by CytoSPADE

Command line instructions:

1) Make sure the first line of this file is your Rscript path (found in the same directory as R)

2) Move the entire directory containing this script and the FCS file(s) to be analyzed to the computer on which you will run SPADE

3) In a command shell, navigate to the folder containing this script and the FCS file(s) to be analyzed

4) Make this script executable. At the command line, run:

$ chmod +x runSPADE.R

5a) For normal use (not in a load sharing or compute cluster): At the command line, run:

$ ./runSPADE.R [-num_threads=X] [-file_to_process=Y]

where X is the number of threads you wish to use (default = 1)

Y is the name of the file to process (default = use file(s) specified in this script)

Note that parameters in brackets may be omitted.

5b) For Sun Gridengine: At the command line, run:

$ qsub -cwd -j y -b y -m e -M username@domain.ext [-pe threaded A] ./runSPADE.R [-num_threads=X] [-file_to_process=Y]

where username@domain.ext is your e-mail address to e-mail when the job is done,

A is the number of slots to reserve with Gridengine,

X is the number of threads to use in SPADE (usually the same as A) (default = 1).

Y is the name of the file to process (default = use file(s) specified in this script)

Note that parameters in brackets may be omitted.

5c) For Platform LSF: At the command line, run:

$ bsub [-n A -R "span[hosts=1]"] ./runSPADE.R [-num_threads=X] [-file_to_process=Y]

A is the number of slots to reserve with LSF,

X is the number of threads to use in SPADE (usually the same as A) (default = 1).

Y is the name of the file to process (default = use file(s) specified in this script)

Note that parameters in brackets may be omitted. (Note that the brackets surrounding "hosts=1" do not indicate an optional parameter.)

Interactive instructions:

1) Move the entire directory containing this script and the FCS file(s) to be analyzed to the computer on which you will run SPADE

2) In an interactive R session, change the working directory to the folder created in step 1

3) At the R command line, run: source("runSPADE.R")

BEGIN AUTOGENERATED DATA

END AUTOGENERATED DATA