Bionic Visualizations
Proteomaps - Issues
To support the generation of user defined treemap layouts we provide the following workflow:
  1. Choose an organism (from the list of models) or provide a species name. This will later help you find your treemap template in the list of user defined layouts.
  2. Comments are useful to explain how and why a treemap layout has been constructed. Especially changes of already available treemaps should be explained. This may help for a general improvement of gene/protein functional assignments.
  3. The user name helps us to build the template name in the list of treemap layouts.
  4. Email is optional, if we realize that you have difficulties in constructing treemaps, this helps us to contact you for further explanations.
    Neither the user name nor the email will be made publicly available.
  5. We support two ways how you can submit the treemap data: The tmd (treemap definition) file was defined to support a scripted or manual generation by using your own computer (use a text editor such as notepad++, notepad, emeditor or others). You can save this file (Use Save within your text editor) and upload it by clicking the [browse] button just on this web page. Choose the file by the file chooser and upload it.
  6. Alternatively you can copy and past the text and insert it into the data form field on this page. To see how the tmd file is structured please click the [insert an example]-link just on this page. The form field now shows the organism specific tmd file that is used in our standard ProteoMap application as a template. The file contains a variety of columns (it is a tab separated text file). For further explanations please read the text linked under [Please consider].
If you prepare data files for generating treemap templates, please consider the following issues:

The data files that define the treemap templates are tab delimited text files. For their construction use a spreadsheet program such as Excel or OpenOffice Calc or a text editor such as emeditor, notepad++ or others. The table rows/lines may represent the genes/proteins. The first columns contain the hierarchy information followed by a gene/protein-identifier assignment. Optionally a column containing RGB data for color definition and a column that defines XY coordinates of the treemap cells can be inserted.

example:
category subcategory subsubcategory protein:ID color position
metabolism energy glycolysis eno:P0A6P9 rgb(25,125,32) xy(25,25)
This defines, that the gene/protein eno is linked to the identifyer P0A6P9. The protein eno is furthermore assigned to the functional category metabolism, subcategory energy, subsubcategory glycolysis. The color is defined as a shade of green and the cell is forced to appear at the position x=25 and y=25.

Hierarchy
The first columns define the hierarchy with the first column as the main categories, the second column containing the first sub categorization, the third column the sub sub categorization and so on until you reach the column before the colon ":".

example:
category subcategory subsubcategory
metabolism energy glycolysis
metabolism energy citric acid cycle
metabolism energy pyruvate DH
The three different subsubcategories glycolysis, citric acid cycle, pyruvate DH were assigned to the same category and subcategory..

Genes/Proteins and Identifyer
The column before ":" describes the deepest level within the hierarchy (mostly the genes/proteins). For a later assignment of cell size data the column following the ":" contains a unique protein ID. For the treemap generation at a later stage the protein ID is important for assigning the cell size (quantitative) data to the correct protein. Furthermore the protein ID is optionally important to interactively link the treemap cell to external databases such as KEGG or others. Database links that support URLs such as http://database?ID will be supported later.

example:
protein:ID
eno:Q29LQ4
Protein ID assignments are given as the protein name (this will be shown in the treemap as label of a polygon) followed by a colon ":" and the protein ID.

Color of treemap cells
The ID column is followed by optional columns in arbitrary order. One column contains the color definition of the treemap cells in the syntax rgb(0-255,0-255,0-255). The RGB-Tag makes clear: The following chain of values defines a color. Comma separated values define the Red, Green and Blue components in the RGB color model. rgb(255,51,54) for example defines a shade of red. It is not necessary to provide RGB codes for all treemap cells. Cells of an upper hierarchy branch can be colored as a whole by providing RGB data.

example
category subcategory subsubcategory protein:ID color
metabolism energy glycolysis eno:P0A6P9 rgb(25,125,32)
metabolism energy rgb(25,125,32)
the first line following the table header defines the rgb(25,125,32) exactly for the cell representing eno
the second line defines shades of rgb(25,125,32) for all cells assigned to the subcategory energy.

Position of a treemap cell
A further optional column may define the X and Y ccordinate where a treemap cell should appear in the generated treemap. The x and y coordinates refer to the top left corner. Values in the range from 0 to an arbitrary valued are supported. Note that the treemap generation is an iterative procedure and is forced to map the correct quantitative data as cell sizes. This may be in contradiction with the given x and y coordinates. By this reason the xy coordinates cannot be guaranteed to force the appearance of the treemap cells at exactly the defined position. xy(25,25) force the treemap cell to appear in the center of the top left treemap quadrant.