If you prepare tmd 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.
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Hierarchy
The first columns define the hierarchy with the first column as the main category, 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.
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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 https://database?ID are explained in the help tooltip for the "db link" form field.
example:
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protein:ID |
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eno:Q29LQ4 |
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| 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.
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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.
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Position of a treemap cell
A further optional column may define the X and Y cordinate 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.
example:
| category |
subcategory |
subsubcategory |
protein:ID |
|
position |
| metabolism |
energy |
glycolysis |
eno:P0A6P9 |
|
xy(25,25) |
| metabolism |
energy |
|
|
|
xy(50,50) |
the first line following the table header defines the position xy(25,25)
for the cell representing eno,
the second line defines xy(50,50) as center of the subcategory energy.
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