| 2fd38c1 | mountainpenguin | 07 March 2017, 09:48:07 UTC | Updated lineage to latest commit | 07 March 2017, 09:48:07 UTC |
| 8fe2a5b | mountainpenguin | 03 February 2017, 17:54:59 UTC | Reworked attempt at diffusion constants for ParB (separated by old/new poles) | 03 February 2017, 17:54:59 UTC |
| f213275 | mountainpenguin | 03 February 2017, 17:54:24 UTC | Add shared method for interpreting wanted.json file | 03 February 2017, 17:54:24 UTC |
| 4f0b48c | mountainpenguin | 31 January 2017, 17:00:07 UTC | Allow custom filters for spot numbers in ParB_velocity to replace two_spot parameter | 31 January 2017, 17:00:07 UTC |
| a643163 | mountainpenguin | 31 January 2017, 16:59:08 UTC | Add code for parAB_comovement -> plots of distance from ParA vs ParB interframe step size | 31 January 2017, 16:59:08 UTC |
| c79ba22 | mountainpenguin | 25 January 2017, 15:58:48 UTC | Re-order priorities (again) | 25 January 2017, 15:58:48 UTC |
| 2adab64 | mountainpenguin | 25 January 2017, 15:37:02 UTC | Add new priorities to todo | 25 January 2017, 15:37:02 UTC |
| 589b24c | mountainpenguin | 25 January 2017, 15:32:48 UTC | Update todo file | 25 January 2017, 15:32:48 UTC |
| c04f341 | mountainpenguin | 25 January 2017, 15:27:33 UTC | Implement parB_distribution script Shows distance of ParB spots from the new pole (at birth) separating by total number of spots and strain | 25 January 2017, 15:27:33 UTC |
| c635f99 | mountainpenguin | 25 January 2017, 15:26:24 UTC | Ignore delta ParA cells in parA_inheritance, and plot children in different colours on jointplot (with all cells as a single regression line) | 25 January 2017, 15:26:24 UTC |
| 7ce4aa4 | mountainpenguin | 25 January 2017, 15:25:50 UTC | Add shebang to parAB_comovement | 25 January 2017, 15:25:50 UTC |
| a7bd4da | mountainpenguin | 24 November 2016, 10:49:52 UTC | parB_distribution: New script for plotting ParB distribution at birth (at least initially) | 24 November 2016, 10:49:52 UTC |
| 2f5d03d | mountainpenguin | 24 November 2016, 10:47:04 UTC | parB_midcell: New script that counts how many cells have ParB foci close to midcell at birth when born with a single focus | 24 November 2016, 10:47:04 UTC |
| be3df12 | mountainpenguin | 24 November 2016, 10:46:40 UTC | parA_inheritance: Use smoothed max ParA intensity instead of absolute value | 24 November 2016, 10:46:40 UTC |
| 3ce5757 | mountainpenguin | 24 November 2016, 10:46:02 UTC | spot_process: Allow processing more than 100 cells, and order by lineage number | 24 November 2016, 10:46:02 UTC |
| 226bde2 | mountainpenguin | 24 November 2016, 10:45:22 UTC | Use general area method for determining drawing area of cells in spot_process | 24 November 2016, 10:45:22 UTC |
| 6407aee | mountainpenguin | 24 November 2016, 10:43:18 UTC | Add ParA analysis to parB_velocity | 24 November 2016, 10:43:18 UTC |
| 6fdc3bf | mountainpenguin | 11 July 2016, 18:55:05 UTC | Updated to parB_velocity - Allow restricting dataset to only cells which start with one spot and end with two, via a `-r` command-line flag - Measure distance between each ParB focus and the ParA peak - Determine, classify, and plot relative ParA/ParB velocities - Rename "stationary" to "static" - Add ttests for New towards vs New away, and Old towards vs Old away - Only plot ttest between New towards and Old towards if p-value is less than 0.05 - Add plot that aggregates velocity counts: -- For ParB: total moving vs total static -- For ParAB: total moving towards or static vs total away - Add matrix plot for ParA/B and ParB classifications | 11 July 2016, 19:00:21 UTC |
| 7e0505e | mountainpenguin | 11 July 2016, 18:48:43 UTC | Update to parA_inheritance Allow for alternative maximum ParA determination method. Remove Y/n mechanic for selecting data, use wanted.json file instead | 11 July 2016, 18:48:43 UTC |
| 83902d9 | mountainpenguin | 27 May 2016, 11:27:57 UTC | Functional parB_minicell script | 27 May 2016, 11:27:57 UTC |
| a6e53b1 | mountainpenguin | 27 May 2016, 11:04:42 UTC | Add initial script for determining whether cells without ParB are also minicells | 27 May 2016, 11:04:42 UTC |
| d4e3855 | mountainpenguin | 27 May 2016, 10:54:25 UTC | First commit for determining parB movement vs diffusion Placeholder file for parAB_comovement | 27 May 2016, 10:54:25 UTC |
| 9f5cce0 | mountainpenguin | 27 May 2016, 10:52:09 UTC | Various style changes parA_inheritance: plot swarm mean values change 'Sibling' to 'Sister' in xlabels parB_velocity: use new colour scheme for bar charts calculate p-value for velocities and annotate them fix x and y labels | 27 May 2016, 10:52:09 UTC |
| 60eb043 | mountainpenguin | 25 May 2016, 12:12:16 UTC | Change axes labels for length and area in parA_inheritance to um | 25 May 2016, 12:12:16 UTC |
| 9a1f277 | mountainpenguin | 24 May 2016, 17:14:56 UTC | Style fixes | 24 May 2016, 17:14:56 UTC |
| c9abaa6 | mountainpenguin | 24 May 2016, 17:10:18 UTC | Rework of spot plot and ancestry styling - remove graph from ancestry plot - change ParA/ParB spot indicator to a triangle outside the cell boundary - add a depiction of the first cell on the left of all plots - fix font size of cell numbering in plots - make ParB traces work in B&W -- light gray lines and markers, with black centre for all markers | 24 May 2016, 17:10:18 UTC |
| fe255be | mountainpenguin | 24 May 2016, 17:08:13 UTC | Allow saving pre-processed data in parB_velocity and add some t-tests | 24 May 2016, 17:08:44 UTC |
| 2714bf5 | mountainpenguin | 24 May 2016, 17:07:01 UTC | Add n values to parA_inheritance plots | 24 May 2016, 17:07:01 UTC |
| 8ea248b | mountainpenguin | 24 May 2016, 17:05:17 UTC | Move get_elongation_rate and add_stats into shared library | 24 May 2016, 17:05:17 UTC |
| 8989e40 | mountainpenguin | 17 May 2016, 18:41:30 UTC | Major rework of parA_inheritance - Store much more data in pandas DataFrame all ratios stored as longer sibling:shorter sibling previously: child_ratio: ratio of total ParA between siblings length_ratio: ratio of sibling lengths area_ratio: ratio of sibling areas added data: max_ratio: ratio of maximum ParA between siblings parent_growth: parental growth rate child1_growth: longer child growth rate child2_growth: shorter child growth rate {parent,child1,child2}_elongation: elongation rate child{1,2}_split: time until first ParB split (if any) {parent,child1,child2}_length: cell length {parent,child1,child2}_area: cell area child{1,2}_total: total ParA intensity for each child child{1,2}_max: maximum ParA intensity for each child - Allow resorting data to split child1/2 by other ratios (e.g. max_ratio instead of length_ratio) - Add swarm plots for plotting comparisons between absolute values between sibling pairs (`swarm`, `swarm2`, `plot_swarms`) - Add more detailed comparisons between sibling pairs (`versus`) - Function for annotating graphs with least-sq fits (`add_stats`) - Add function for determining ParB split time (`get_parB_split`) - Allow choosing which directories will be included in the analysis - Function for sanity checks of data resorts (`sanity_check`) - Function for plotting ratios (`plot_ratios`, previously written within `main`) - Function for comparing representations (max_ratio sorting vs length_ratio sorting: `plot_representation`) | 17 May 2016, 18:41:30 UTC |
| 8b4eebf | mountainpenguin | 11 May 2016, 22:39:33 UTC | Save ParB velocity data to Excel Also rename growth_rate to elongation_rate | 11 May 2016, 22:39:33 UTC |
| b371054 | mountainpenguin | 11 May 2016, 22:37:49 UTC | Style fixes for parB_interspot | 11 May 2016, 22:37:49 UTC |
| 97e56e6 | mountainpenguin | 11 May 2016, 10:26:23 UTC | Add script for analysis of parB separation velocity (i.e. interspot distance over time) | 11 May 2016, 10:26:23 UTC |
| 35bac29 | mountainpenguin | 10 May 2016, 14:47:40 UTC | Update todo | 10 May 2016, 14:47:40 UTC |
| 2bb2778 | mountainpenguin | 10 May 2016, 13:58:37 UTC | Make polefix actually work | 10 May 2016, 13:58:37 UTC |
| 3c916fe | mountainpenguin | 10 May 2016, 13:57:17 UTC | Make sure spots aren't ignored if the new pole is correctly assigned as index 0 in the cell mesh Also make sure that lineage numbers above 100 are processed by spot_connect | 10 May 2016, 13:57:17 UTC |
| 0f02016 | mountainpenguin | 10 May 2016, 13:56:41 UTC | Fix padding scaling in um plots | 10 May 2016, 13:56:41 UTC |
| 7847c24 | mountainpenguin | 05 May 2016, 22:29:53 UTC | Style fix | 05 May 2016, 22:29:53 UTC |
| cb49c45 | mountainpenguin | 05 May 2016, 22:27:51 UTC | Allow for empty datasets in parB_velocity | 05 May 2016, 22:27:51 UTC |
| dbf8c95 | mountainpenguin | 05 May 2016, 22:27:17 UTC | Allow selecting um or px mode to allow spot_process to work Also modify spot_plot for ParB only plots in um | 05 May 2016, 22:27:17 UTC |
| 45ed274 | mountainpenguin | 02 May 2016, 12:48:00 UTC | Label new pole on spot plots / spot_ancestry plots (red if unknown, blue if known) | 02 May 2016, 12:48:00 UTC |
| 25b77a4 | mountainpenguin | 02 May 2016, 12:47:15 UTC | Annotate daughter cell numbers on spot plots. Use simple cell numbers for ancestry titles (instead of A, AB, etc notation) | 02 May 2016, 12:47:15 UTC |
| b28a0b7 | mountainpenguin | 02 May 2016, 12:45:59 UTC | Convert spot_ancestry plots (and individual spot plots) to use um. | 02 May 2016, 12:45:59 UTC |
| 5edcb4f | mountainpenguin | 27 April 2016, 16:27:10 UTC | Plot regression lines on parA_inheritance plots | 27 April 2016, 16:27:10 UTC |
| 31fc401 | mountainpenguin | 26 April 2016, 18:53:52 UTC | Allow moving back a cell in spot_process | 26 April 2016, 18:53:52 UTC |
| ecbbf6c | mountainpenguin | 26 April 2016, 18:52:58 UTC | Plot velocities relative to mid-cell for spots moving *away* relative to a pole | 26 April 2016, 18:52:58 UTC |
| 9b81c4d | mountainpenguin | 26 April 2016, 18:52:20 UTC | Use LaTeX in parB_velocity plots and clean up prefixing | 26 April 2016, 18:52:20 UTC |
| 9de7b7a | mountainpenguin | 13 April 2016, 14:28:43 UTC | Update todo (remove ParA partitioning) | 13 April 2016, 14:28:43 UTC |
| fc7a02b | mountainpenguin | 13 April 2016, 13:37:01 UTC | Store data and show distributions in parA_inheritance - store data as pandas DataFrame for reuse/replotting - show 4 plots: scatter: intensity ratio (child_ratio) vs area ratio (area_ratio) scatter: intensity ratio (child_ratio) vs length ratio (length_ratio) histogram: child_ratio / area_ratio histogram: child_ratio / length_ratio | 13 April 2016, 13:37:01 UTC |
| 8b0a6d0 | mountainpenguin | 11 April 2016, 18:12:55 UTC | Extend and improve parA_inheritance - Apply inheritance measurements to all applicable directories - Plot ratio in child ParA intensity vs ratio in child length/area | 11 April 2016, 18:12:55 UTC |
| 97aa3a2 | mountainpenguin | 08 April 2016, 17:26:34 UTC | First step towards measuring asymmetry in ParA partitioning | 08 April 2016, 17:26:34 UTC |
| 4fc37ad | mountainpenguin | 06 April 2016, 15:07:19 UTC | Reorder todo priorities | 06 April 2016, 15:07:19 UTC |
| f9bfc11 | mountainpenguin | 05 April 2016, 20:06:02 UTC | Add legends to parA_distribution Colourbar for distribution heatmap, and coloured lines for lower plot | 05 April 2016, 20:06:02 UTC |
| 4a06017 | mountainpenguin | 05 April 2016, 13:55:56 UTC | Update todo | 05 April 2016, 13:55:56 UTC |
| 3ad3557 | mountainpenguin | 05 April 2016, 13:34:46 UTC | Update lineage reference | 05 April 2016, 13:34:46 UTC |
| 34d114f | mountainpenguin | 22 March 2016, 23:08:30 UTC | Update lineage reference | 22 March 2016, 23:08:30 UTC |
| 83b4a41 | mountainpenguin | 22 March 2016, 22:59:29 UTC | Update parB_velocity to consume much less memory and allow grouping strains. No longer stores all `cell_line` objects at once, loads them as needed from the numpy files. Now also requires the `poles.json` file to be present in the working directory (i.e. poles are assigned). Adds a new function `run()` which performs velocity measurements, plots traces, stats, and examples on a working directory. Adds a `-g` flag for grouping similar strains according to the `groupings.json` file in the root directory. | 22 March 2016, 22:59:29 UTC |
| fbe1cbf | mountainpenguin | 22 March 2016, 21:06:36 UTC | Update file naming for ParA dist and ParB velocity and update todo list | 22 March 2016, 22:59:17 UTC |
| 5f707f9 | mountainpenguin | 16 March 2016, 14:45:02 UTC | Add a nicer method of debug output generation (commented out). | 16 March 2016, 14:45:02 UTC |
| 3bdf2f5 | mountainpenguin | 16 March 2016, 14:43:53 UTC | Allow parB_velocity threshold to be set to 0 Reduce number of plots if so (i.e. don't show data for stationary direction). Also add a dotted vertical line at the 0 position on velocity histograms. | 16 March 2016, 14:43:53 UTC |
| 8fd9e97 | mountainpenguin | 16 March 2016, 14:40:42 UTC | Allow plotting examples via hashing system Separate `plot_traces` into `plot_traces` and `plot_stats` for individual PDF outputs. Add `plot_examples` function for plotting example traces: 3 random examples for each `tether` and each `direction`, as well as the highest velocity trace (i.e. 4 for each `tether` and `direction` combination). | 16 March 2016, 14:43:16 UTC |
| 103be30 | mountainpenguin | 14 March 2016, 22:57:13 UTC | Use a dedicated directory for saving ParA distributions, and encode information more readably in filenames | 14 March 2016, 22:57:13 UTC |
| 4b15ab6 | mountainpenguin | 14 March 2016, 22:47:01 UTC | Fixes for parB_velocity get_velocities: - change threshold (`THRESHOLD`) to 0.1 um / hr - change minimum points (`MIN_POINTS`) in a ParB trace to 5 - remove debugging plot for velocity determination - add an absolute parameter (`v_abs`) for velocities, relative to the tether, i.e.: * if tether is new pole, `v_abs = abs(v_new)` * if tether is old pole, `v_abs = abs(v_old)` - change tether to `None` if final position is exactly 0 (i.e. can't be assigned to either new or old pole) _plot: - colour velocities lower than the threshold red on plotted histograms - return representative patches for stationary and moving spots for subsequent labelling plot_traces: - use a dedicated directory for saving PDFs - save `THRESHOLD` and `MIN_POINTS` information in file names -- distribution plots - share xy limits between velocity plots depicting both directions (column 0) - share xy limits between directional velocity plots (columns 1 and 2) - add plot legends of n-values for all sub-divisions of data - set sane xlimits and xticks -- stats plots - plot by tethered pole rather than by direction (x subdivision) - use direction as a hue instead | 14 March 2016, 22:47:01 UTC |
| 375dc72 | mountainpenguin | 11 March 2016, 22:25:27 UTC | Temp fixes for parB_velocity | 11 March 2016, 22:25:27 UTC |
| 24d01e3 | mountainpenguin | 10 March 2016, 14:21:55 UTC | Plot ParB velocities (without growth rate correction) | 10 March 2016, 14:21:55 UTC |
| 769befd | mountainpenguin | 08 March 2016, 19:57:43 UTC | First implementation of parB_velocity: general plots only | 08 March 2016, 19:57:43 UTC |
| 4320b4b | mountainpenguin | 08 March 2016, 13:41:34 UTC | Normalise ParA intensity per cell rather than per bin. | 08 March 2016, 13:41:34 UTC |
| 68cb56f | mountainpenguin | 08 March 2016, 13:23:28 UTC | Fix cell cycle binning for a more even distribution. Adjust default number of bins to 10. Plot number of cells in each bin in a subplot above heatmap. Plot traces of ParA distribution at all cell cycle points on a subplot below the heatmap. Also add todo to separate daughters that receive high levels of ParA from those that receive low levels for distribution plots. | 08 March 2016, 13:23:28 UTC |
| bb24061 | mountainpenguin | 07 March 2016, 22:14:33 UTC | Temporarily disable parA_distribution until cell cycle assignment can be confirmed. | 07 March 2016, 22:14:33 UTC |
| d500b87 | mountainpenguin | 07 March 2016, 22:14:15 UTC | Save settings in parA distribution filename | 07 March 2016, 22:14:15 UTC |
| 3f0ea62 | mountainpenguin | 07 March 2016, 22:03:10 UTC | Update todo | 07 March 2016, 22:03:10 UTC |
| 1242c0e | mountainpenguin | 07 March 2016, 22:01:23 UTC | Add a proper method of resampling histograms and make length bins variable. Portion out bins according to overlap between old and new bin sizes. Determine number of length bins by the largest number in the data set, so all cells are scaled to the largest cell. | 07 March 2016, 22:02:00 UTC |
| f254c88 | mountainpenguin | 07 March 2016, 17:11:01 UTC | Enable addition of non-complete cell lines to parA distributions, as well as collation of all available data sources. If a cell line has no parent, but has a pole assignment *and* has children, its last cell (just before division) can be assigned to the last cell cycle bin. If a cell line has a parent (i.e. observed division event), but has no children, its first cell (just after division) can be assigned to the last cell cycle bin. Use `wanted.json` to define top-level directories to extract all available cell lines. | 07 March 2016, 17:11:01 UTC |
| 4d6e3ad | mountainpenguin | 07 March 2016, 15:41:59 UTC | Update lineage | 07 March 2016, 15:41:59 UTC |
| c46c3fe | mountainpenguin | 07 March 2016, 15:41:33 UTC | Update lineage | 07 March 2016, 15:41:33 UTC |
| 8469c7a | mountainpenguin | 07 March 2016, 15:39:15 UTC | Use seaborn and label axes for parA distribution plots | 07 March 2016, 15:39:53 UTC |
| 881b3a1 | mountainpenguin | 01 March 2016, 00:45:05 UTC | Update lineage | 01 March 2016, 00:45:05 UTC |
| 8e13076 | mountainpenguin | 01 March 2016, 00:34:25 UTC | Update lineage | 01 March 2016, 00:34:25 UTC |
| 6f05872 | mountainpenguin | 29 February 2016, 22:18:23 UTC | Make sure pole assignments and orientation reversals are correctly applied during spot_analysis Also indicate new pole in spot_process | 29 February 2016, 22:18:23 UTC |
| ffd3d69 | mountainpenguin | 28 February 2016, 20:32:37 UTC | Update lineage ref | 28 February 2016, 20:32:37 UTC |
| ddf679e | mountainpenguin | 28 February 2016, 20:29:49 UTC | Add first attempt at ParA distribution plotter Add placeholder file for ParB velocity measurements | 28 February 2016, 20:29:49 UTC |
| 71128d4 | mountainpenguin | 28 February 2016, 20:29:20 UTC | Add central line reversal in polefix just in case -- must check! | 28 February 2016, 20:29:20 UTC |
| 0e079b5 | mountainpenguin | 28 February 2016, 17:35:33 UTC | Add script for fixing pole assignments in existing datasets Note: destroys pole data saved by spot_connect script | 28 February 2016, 17:35:33 UTC |
| e1b7928 | mountainpenguin | 28 February 2016, 16:06:33 UTC | Really allow not plotting graphs | 28 February 2016, 16:06:33 UTC |
| 5fe6b73 | mountainpenguin | 28 February 2016, 16:05:26 UTC | Use pole assignments in spot_analysis routine Replace orientation with mesh reversals If new pole is assigned to last mesh point, then reverse mesh again to make new pole first mesh point | 28 February 2016, 16:05:26 UTC |
| 5558695 | mountainpenguin | 26 February 2016, 09:30:43 UTC | Update lineage | 26 February 2016, 09:30:43 UTC |
| 96b8492 | mountainpenguin | 25 February 2016, 23:48:49 UTC | Add todo item | 25 February 2016, 23:48:49 UTC |
| d1edbf1 | mountainpenguin | 25 February 2016, 15:10:11 UTC | Update lineage | 25 February 2016, 15:10:11 UTC |
| 2089994 | mountainpenguin | 25 February 2016, 00:22:59 UTC | Reverse submodule testing changes | 25 February 2016, 00:22:59 UTC |
| 6ce3411 | mountainpenguin | 25 February 2016, 00:19:01 UTC | Re-rename .gitmodule to .gitmodules | 25 February 2016, 00:19:01 UTC |
| 4f96cbc | mountainpenguin | 25 February 2016, 00:17:25 UTC | Testing | 25 February 2016, 00:17:25 UTC |
| 6409f53 | mountainpenguin | 25 February 2016, 00:15:19 UTC | Test rename | 25 February 2016, 00:15:19 UTC |
| f4ea407 | mountainpenguin | 25 February 2016, 00:13:04 UTC | Specify master branch for submodule lineage | 25 February 2016, 00:13:04 UTC |
| 20e45cc | mountainpenguin | 25 February 2016, 00:01:04 UTC | Update todo | 25 February 2016, 00:08:06 UTC |
| 9fb39de | mountainpenguin | 24 February 2016, 23:59:56 UTC | Fix spot_process centering and intensity scaling Make sure x and y limits are correct way around when at image boundaries Use polygon of cell outline for determining intensity scaling | 24 February 2016, 23:59:56 UTC |
| 5ab7d2a | mountainpenguin | 18 February 2016, 22:16:04 UTC | Update todo | 18 February 2016, 22:16:04 UTC |
| 736d86e | mountainpenguin | 18 February 2016, 22:15:49 UTC | Add remove all key binding to spot_process | 18 February 2016, 22:15:49 UTC |
| f698f13 | mountainpenguin | 18 February 2016, 22:15:21 UTC | Allow defining images/graphs only in spot_plot | 18 February 2016, 22:15:21 UTC |
| cbfd854 | mountainpenguin | 18 February 2016, 22:14:34 UTC | Add network graph to ancestry plots to establish relationships between cells | 18 February 2016, 22:14:34 UTC |
| db96e68 | mountainpenguin | 18 February 2016, 22:13:54 UTC | Allow plotting both ancestry and normal plots in plot_wanted script | 18 February 2016, 22:13:54 UTC |
