"Mutational spaces for leaf shape and size"
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To create the figures shown in the manuscript “Mutational spaces for leaf shape and size”, S. Bensmihen, A. I. Hanna, N. B. Langlade, J. L. Micol, A. Bangham, and E. S. Coen, HFSP Journal, 2008, please follow the instructions below.
These figures were created using Matlab 2006b version 7.3.0.267 running on Windows XP.
Installing the toolbox
To install the toolbox, simply unzip the zip file you downloaded from the website. In that folder you will find 2 folders, the first one will be the ‘AAMToolbox’ folder (this contains the Matlab files that runs the toolbox). The second folder is named ‘PRJ_Arabid_Antirrh’. This is the project folder that contains all the data for the manuscript. To install the toolbox, from the Matlab prompt type
>>pathtool
Click the ‘Add with subfolders’ button and then select the AAMToolbox folder. Save your new path and return to Matlab. You have now installed the toolbox. REMEMBER, ANY CHANGES YOU MAKE TO THE TOOLBOX DIRECTORY WILL REQUIRE YOU TO RESET THE PATH USING PATHOOL.
Creating Figures
Figure 1
From the Matlab prompt type
>>figure_1_points_around_leaf
And select LE50template_04_05_06.temp_dat from the Templates directory. The colours are your choice.
Figure 2
From the Matlab prompt type
>>figure_2_pc_effects
- Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_18’ for model (Ler only, not scaled).
- Next choose the PCs you want to display (1 to 5 in our case).
- Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).
Figure 3
From the Matlab prompt type
>>AAMToolbox
- Make sure that the current model is “LE50Template_04_05_06\Set_1\ImageList_18” from the drop down list.
- Next click the “View Shape Space” button.
- Next click the “Open” button from the Groups panel and select “all_groups_no_tsk”.
- Next click the “Load” button from the Groups panel.
- Next select ‘Tools-Units-Standard Deviations’.
- Next uncheck the “Group Labels” from the plot options panel.
- Next click the “Choose Shape Axes” button and select the PC 1. (To view another PC click the “Choose Shape Axes” button and choose the PC of interest (in our case PC1, PC2, PC3, PC4).)
Figure 4
UNDER CONSTRUCTION
Figure 5
From the Matlab prompt type
>>figure_2_pc_effects
- Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_17’ for model (Ler only, scaled).
- Next choose the PCs you want to display (1 to 4 in our case).
- Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).
Figure 6
From the Matlab prompt type
>>figure_2_pc_effects
- Select the folder ‘PRJ_Arabid_Antirrh\StatisticalModels\LE50Template_04_05_06\Set_1\ImageList_21’ for model (_epure= cleaned form double mutant and flower effect mutants).
- Next choose the PCs you want to display (1 to 4 in our case).
- Next choose to use the mean from the model and finally select 2SD range. (The vertical and horizontal ranges can be changed but the default gets you started).