nolanlab/cytospade

Cytoscape plugin for SPADE

cytospade's Issues

Make T test table and biaxial plots pop-outable, instantiable

(1) Make the T test table and biaxial plots pop-out-able
(2) Make it possible to have as many biaxials as you want.

Plugin not entirely international-safe

The plugin generates numeric transformation parameters that use commas as the decimal separator when run under certain locales. R can't handle this, even when run under those same comma-as-decimal locales.

See: nolanlab/spade#34 (comment)

Make layout stored in GML file instead of layout.table

Store the node coordinates in the GML graphlet files instead of in the layout.table file.

Low-priority, but want to keep this in mind as we start storing annotations, so that we don't end up with (1) an FCS file, (2) a GML file, (3) a layout.table file, (4) an annotations file ... when we could just have an FCS and GML.

Fix background (renderer) for filename combobox

A custom renderer is used for the filename combobox in the WEST panel. Fix it so the background isn't white.

Node layout is occasionally lost

One in maybe 10 times of loading a Cytoscape/Cytospade project, the layout is lost and all nodes become concentric. The layout.table file is entirely {0.0 -0.0} when this happens. So far I haven't figured out under what circumstances this happens. If anyone else has noticed when this tends to happen, please comment.

One guess: the saveMetadata(false) method is called before the network is fully loaded, and all nodes have a 0,0 position.

Hierarchically nested nodes do not produce biaxial plots, stats

With Ketaki's latest revisions, it's possible to make hierarchically nested nodes. Selecting a singly nested node produces the biaxial plot and T values for the events contained in the constituent nodes. Selecting a hierarchically nested node does not.

I'm not seeing why this is happening at first glance.

downsampling_samples bug with the new spade version

the plugin generates a script that calls an unused argument

SPADE.driver(...downsampling_samples...

(src/cytospade/SpadeContext.java line 581)

that gives the following error:

unused argument (downsampling_samples = DOWNSAMPLED_EVENTS)
Execution halted

Add symmetric color scale option

Add option to make color scale symmetric, e.g. +/- (Max[Abs[attributeValues]]).

Unable to load CytoSPADE.dist.jar

Hello everyone,
I have a problem with the CytoSPADE plugin form the cytoscape3 branch.
I successfully built the jar file, using NetBeans, I copied the CytoSPADE.jar.dist into the plugins folder and I restart the Cytoscape software. The plugin is no longer available into the program and if I try to install it from the Cytoscape interface, it gives to me a lot of errors.

How can I fix it? Are there any suggestions? I tried both on linux and mac os x.

Thank you!

Bold T test params used for clustering

If a T test parameter was used for clustering, make it bold.

Unable to load trees

Hi everyone,
I have a problem with cytospade, on my Linux Machine.
I'm able to generate the output folder, but I cannot load this folder into cytospade, to analyze data.

Any help would be appreciated!

Stefano

CytoSPADE Plugin Issues

Hi All,

I have recently installed the spade R package and have had some early success in working through the pipeline with my own data. However, in an effort to make the package more accessible to the rest of my lab, I'm trying to move to the Cytoscape plugin rather than the R interface, but I'm unfortunately facing some issues:

When installing the plugin from R, everything seems to go smoothly and I get the expected "plugin has installed correctly" message.

In Cytoscape, I'm able to open the plugin, select files, choose markers for clustering and enter values for the sampling parameters.

My issue is that once at the "run" screen, pressing either Generate run spade script, or run Spade does nothing at all. In my working directory, the runSPADE.R script is generated but it is completely empty.

I am have tried this is both Cytoscape 2.8.2 and 2.8.3 with the same issue. I'm running R version 3.0.1 on 64bit Windows 7. I have also made sure to run R and Cytoscape as administrator to avoid weird permission issues.

Any help would be greatly appreciated!!

Fred

Unused argument -- downsampling_samples = DOWNSAMPLED_EVENTS

Hello, I have just started begun trying to use CytoSPADE and have been unable to successfully generate a tree using the sample data.

The revenant error is:

"Error in SPADE.driver(FILE_TO_PROCESS, file_pattern = "*.fcs", out_dir = OUTPUT_DIR, :
unused argument (downsampling_samples = DOWNSAMPLED_EVENTS)
Execution halted"

I know this error has been documented before, but I am not sure how to fix it. I have reinstalled SPADE (and the plugin) and Cytoscape several times.
I am running Cytoscape 2.8.3, SPADE 1.12.0, and R 3.1.0 on Mac. Thank you!

Only top 8 values shown in T-test pane in commit baaa5c81ea

Title pretty much says it all -- the T-test pane in baaa5c81ea only shows the top 8 values. It would be nice to have all of them -- is this too computationally expensive?

Use 2nd to 98th percentile color scales

The iGraph color scale goes from 2nd to 98th percentile. The CytoSPADE plugin does not.

Implementation:
https://github.com/nolanlab/spade/blob/master/R/driver.R:418