Scripts and plots from: "A comparative analysis of spindle morphometrics across metazoans" or #SpindleZoo.
In the spirit of #OpenScience, our complete data set (measurements) and R and Python code generated in the course of data analysis is deposited here. We are working on making the raw data (images) available too. We will provide a link here once we manage to do so.
You are free to use data and code for scientific and educational purposes. We only ask you to cite the paper!
####DATA FILES
All data files are in the folder Final/Data.
The raw data file was: ZOODATA_140923.xlsx. The 'clean data' version of this file is: original.csv.
There is a number of modified files we saved along the way. They are all in this directory. df2_original_for_SQL.csv contains mostly 'clean' data. The same is true for original.csv. They differ with respect to the types of categorical columns. original.csv has 41 columns. All catergorical columns have a an equivalent ending with 'CAT', which encodes strings (words) with integers.
Two files: meiotic_false.csv and meiotic_true.csv are the result of splitting the original data frame on the column meiotic (i.e. whether spindles are meiotic or mitotic). The final two files: mitotic_anaphase.to_csv and mitotic_metaphase.csv are the result of and additional data split in file meiotic_true.csv on the column stage (i.e. stage of the cell cycle). SQLite database (df2_original.db) contains the same data as in the file: df2_original_for_SQL.csv; title of the table is data_for_DB.
There are two additionally processed files: original_SQL_WO_dupes_WO_metadata_from_R.csv and original_SQL_metaphase_only_from_R.csv. File original_SQL_WO_dupes_WO_metadata_from_R.csv contains the same data as original.csv but has variables characterizing two sides of the spindle averaged out (see: Spindle_zoo_part_3_.. for details). File original_SQL_metaphase_only_from_R.csv is created from original_SQL_WO_dupes_WO_metadata_from_R.csv but contains metaphase spindles only (both meiotic and mitotic).
Please refer to the file SpindleZooColumnKey.txt for the description of columns.
As of May 2015, Github renders Jupyter notebooks. You should see the ouput (i.e. not raw JSON), when you click the file on-line (have patience, some of them are a bit large and take time to render).
Alternative way to visualize our code is through nbviewer. All files ending with .ipynb can be scrolled through this way (you can see the code and the output). Simply, go to the folder with all our code, right click on the file ending with .ipynb, copy the link address, paste it here and hit Go!.
This is what it should look like.
The code with no plots in the manuscript has a suffix _appendix.
The project site lives here.