Using the cell shape template

To use ‘Cell shape’ template:

1. Upload your data by selecting File-> Load data -> Upload file. Check the Help section for guidelines on data format.
2. Alternatively, you can try our breast cancer cell line dataset: File -> Load data -> Datasets -> Breast Cancer Cell Lines
3. You can view the loaded data by clicking the data button on the top menu
4. A cell will be created for each sample (row in the data file) where each cell is composed of Cell and Nucleus objects which can be seen on the right menu.
5. You can adjust the colour of the ‘Cell’ by selecting the object and using the colour picker in the left menu.
   
   You can also customise other features from the global features meue on the right.
6. Now, you can map the variables/features (columns in the data file) to cell glyphs using the right menu.
7. Select the 'Cell' object from the ‘Objects’ menu on the right. Under 'Data mapping' you can select features to be plotted on the glyphs. Below are examples of how you can map your data to Cell glyph. Note these are all optional (you only choose the mapping that apply to your data)
   • Select length variable to be mapped to Length (e.g. Cell length)
   • Select width variable to be mapped to Width (e.g. Cell width)
   • To represent protein levels that localise in the cytoplasm, click on Fill gradient and select the desired variable. You can also change the colour map.
   • You can also represent protein level using the 'Fill symbols'. You can change the symbol shape, size, colour, and the direction the symbols will be filled. The more symbols filling the cell ellipse correspond to higher protein levels.
   • To represent membrane processes (e.g. Focal adhesion), you can use 'Border symbol'. You can adjust the symbol size or shape.
   • To represent cell adhesion data, click on Border overlay and select your variable (e.g. NF)
8. You can do similar mapping for nuclear proteins and processes. Select the ‘Nucleus’ object on the right menu. Under 'Data mapping' you can select features to be mapped as in the following examples
   • Select length variable to be mapped to Length (e.g. Nucleus length)
   • Select width variable to be mapped to Width (e.g. Nucleus width)
   • To represent protein levels that localise in the nucleus, click on 'Fill gradient' and select the desired variable. You can also change the colour map.
   • You can also represent protein level using the 'Fill symbols'. You can change the symbol shape, size, colour, and the direction the symbols will be filled. The more symbols filling the nucleus ellipse correspond to higher protein levels.
   • To represent processes on the nuclear membrane (e.g. nuclear pore proteins), you can use 'Border symbol'. You can adjust symbol size or shape.
9. You can save your mapping by saving the template: File -> Save template which will save your mapping and created objects to a ‘json’ file. To use the template again, you can select File -> Load project -> Specify your data and template files.

*Note if your data file has different column names, you need to map them again but the same objects will be available.

Tip 1 : You can view the legend from the top menu

Tip 2 : You can edit the template by adding an object. You can change the order using top and down arrows on the left of the object. You can also change the object size using 'Global features'. For example, try to create a square, move it to the top of the object list and map it to cell density.

Tip 3 : If you map size or dimensional data, read our guidelines on normalising dimensional data.