I wanted to use the JFreecharts heatmap node to just graph some data that has already been analyzed in excel. I thought I could just import that and run it through the node, but it is asking for a DistanceVector or a ListCell as input. As far as I can tell, making a distance vector requires more calculation and like I said, the calculations are already done. I can't find any reference to what a ListCell is or how to make it.
I see that I need to have some kind of collection column ultimately, but I don't see how the limited options of the node fit my data.
For example, in the data set, each row represents a clone. I have the following columns:
Column A: Y-axis values, a list of positions, repeating, one value per row
Column B: X-axis values (top row in example), a list of mutations, repeating, one value per row
Column C: Mouse data value (M)
Column D: Human data value (H)
When graphed it should look like this
F L I (Mutations)
H M H M H M (Species)
27 red blue grey grey red red
28 blue blue grey grey red blue
etc...
Hopefully this is understandable. Any suggestions would be much appreciated. I may need to transpose and rearrange some of the input data to make it work with Knime, but I was hoping I could do any such manipulations within the program.
If you need the most simple heatmap, then changing a few column's cell renderer to Gray Scale or Bar would be also sufficient (either in a port view or in an Interactive Table view).
Hi Mark, you are welcome. Although the Simple Heatmap might be also an option (except the column headers cannot be as nice unless youchange the labels with an image editor). The colors can be assigned according to your sample legend, can be saved to SVG or PNG.
i find problem to install hits at site ...some problem this is the message:
Some sites could not be found. See the error log for more detail.
No repository found at http://hits.googlecode.com/svn/.
Unable to read repository at https://code.google.com/p/hits/content.xml.
sun.security.validator.ValidatorException: PKIX path validation failed: java.security.cert.CertPathValidatorException: timestamp check failed
No repository found at http://hits.googlecode.com/svn/trunk/.
Unable to read repository at https://code.google.com/p/hits/downloads/list/content.xml.
sun.security.validator.ValidatorException: PKIX path validation failed: java.security.cert.CertPathValidatorException: timestamp check failed
is there onother site or is it possible to dwnlod the entire zip ?
Hope you do not mind if I try to answer (I developed HiTS). Did you use the http://hits.googlecode.com/svn/trunk/ie.tcd.imm.hits.update update site? What version of KNIME were you using? As I remember for the heatmaps (Heatmap with Dendrogram) you need the following features:
HiTS 3rd party components feature (from HiTS main category)
HiTS main feature (from HiTS main)
If you need the Heatmap with Dendrogram node too, you will have to install the HiTS experimental features (from HiTS main).
Here are the dependencies if you want to use the CellHTS2 or the biomaRt nodes too. (If you want only the heatmaps, you will not need R, CellHTS2 and biomaRt.)
Please send a message or raise an issue if the Dependencies or the Install wiki page contain unclear parts.
I have not created an update site as a zip file yet, because I think that time there was a limitation on file sizes on Google code, but maybe I have just forgotten this possible use case.
(The features, plugins are not signed.)
Cheers, gabor
PS.: I have tried the above mentioned update site, and I was able to read the content with KNIME 2.6.1, I guess older (from 2.4.x as I remember for certain features) KNIME versions (also newer ones) should be fine.
Attached is an an example using your data. I couldn't find a nice way to get teh x-axis labels to show up, but maybe someone else has some feedback there.
I use the last version 2.7.3 ,i checked for depemdency and all is ok. I installed in the past hits pluging and work fine, but this time find problem in connection :
I do not know what could be the problem. Which operating system do you use? Is it 64 or 32 bit? Is your KNIME 64 bit?
I have just tried to install HiTS to a 64 bit Win7 machine with a 64 bit KNIME 2.7.3 from the http://hits.googlecode.com/svn/trunk/ie.tcd.imm.hits.update/ update site (with direct connection to the internet).