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usage:plotting [2019/07/24 13:40] – [Plot export options] pseudomoaner | usage:plotting [2022/09/05 23:05] (current) – pseudomoaner | ||
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- | If you wish to explore a user-generated track-associated dataset using the plotting module, simply save this new dataset as a separate field in procTracks. This field will then become available within the **Data 1 selection** and **Data 2 selection** drop-down menus. An example script that saves each object' | + | If you wish to explore a user-generated track-associated dataset using the plotting module, simply save this new dataset as a separate field in procTracks. This field will then become available within the **Data 1 selection** and **Data 2 selection** drop-down menus. An example script that unwraps |
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The contents of plotExport varies depending on the plot type chosen at the point of data export, but in general it consists of a 4x1 cell array containing a separate structure for each object population. Data corresponding to all objects is stored in cell 1, while data corresponding to populations 1, 2 and 3 (if defined) are stored in cells 2, 3 and 4, respectively. | The contents of plotExport varies depending on the plot type chosen at the point of data export, but in general it consists of a 4x1 cell array containing a separate structure for each object population. Data corresponding to all objects is stored in cell 1, while data corresponding to populations 1, 2 and 3 (if defined) are stored in cells 2, 3 and 4, respectively. | ||
- | The structures stored within each of these cells are themselves built differently depending on the currently selected plot and the settings currently applied to that plot. For example, with the **Timecourse** option selected and the **Show standard deviation** box checked, cell 1 of the plotExport variable will contain three fields, **times** (the sampled timepoints in physical units), **dataMeans** (the average value of the chosen track-associated dataset at each timepoint) and **dataStd** (the standard deviation of the chosen track-associated dataset across all tracks at each timepoint). When **Show all tracks** is selected however, **times** and **dataMeans** will be replaced with **subTimes** and **subData**, | + | The structures stored within each of these cells are themselves built differently depending on the currently selected plot and the settings currently applied to that plot. For example, with the **Timecourse** option selected and the **Show standard deviation** box checked, cell 1 of the plotExport variable will contain three fields, **times** (the sampled timepoints in physical units), **dataMeans** (the average value of the chosen track-associated dataset at each timepoint) and **dataStd** (the standard deviation of the chosen track-associated dataset across all tracks at each timepoint). When **Show all tracks** is selected |
=== Save axes as .fig === | === Save axes as .fig === | ||
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FAST offers a variety of different plotting options. In this section, examples of each of these plots are given, and descriptions of the associated settings provided. | FAST offers a variety of different plotting options. In this section, examples of each of these plots are given, and descriptions of the associated settings provided. | ||
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==== Histograms ==== | ==== Histograms ==== | ||
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* **Show correlation coefficient: | * **Show correlation coefficient: | ||
* **Plot linear fit:** Display a line of best fit through the data points for the selected populations. | * **Plot linear fit:** Display a line of best fit through the data points for the selected populations. | ||
+ | * **Show all sampling points:** Show all the sampled points for each track, rather than the whole-track average. | ||
+ | * **Colour points by local density:** Colours each plotted point according to the density of points in the surrounding region, with high-density regions appearing darker and low-density regions appearing brighter. Particularly useful for datasets containing many tracks and for use in conjunction with the 'Show all sampling points' | ||
{{ : | {{ : | ||
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{{ : | {{ : | ||
- | ==== Cartouche ==== | ||
- | Generates a ' | + | ==== Phase space ==== |
- | Options: | + | Plots tracks, using arbitrary track-associated variables in place of object |
- | * **Track ID:** The ID number | + | |
- | * **Start frame:** The timepoint in the current | + | |
- | * **Length:** The total number of timepoints you wish to display. | + | |
- | * **Align cells?:** Select to rotate all objects in the track such that they all point upwards. Deselect to display objects in their native orientation. | + | |
- | {{ :usage:plotting:cartouche.png? | + | This plotting |
- | ==== Kymograph ==== | + | |
- | Generates a kymograph (space-time plot) of the selected object in all available channels. | + | {{ : |
- | Options: | ||
- | * **Track ID:** The ID number of the displayed object. Can be found by checking **Show IDs?** in the [[usage: | ||
- | * **Equate lengths?:** Select to stretch or compress object profiles to ensure that provile length is constant over time. Deselect to display object profiles at native lengths at all timepoints. | ||
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- | FIXME | ||
==== Event-centred average ==== | ==== Event-centred average ==== | ||
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{{ : | {{ : | ||
+ | ==== Cartouche ==== | ||
+ | |||
+ | Generates a ' | ||
+ | |||
+ | Options: | ||
+ | * **Track ID:** The ID number of the displayed object. Can be found by checking **Show IDs?** in the [[usage: | ||
+ | * **Start frame:** The timepoint in the current track you want display to begin. Measured relative to the start of the track. | ||
+ | * **Length:** The total number of timepoints you wish to display. | ||
+ | * **Align cells?:** Select to rotate all objects in the track such that they all point upwards. Deselect to display objects in their native orientation. | ||
+ | |||
+ | {{ : | ||
+ | ==== Kymograph ==== | ||
+ | |||
+ | Generates a kymograph (space-time plot) of the selected object in all available channels. | ||
+ | |||
+ | Options: | ||
+ | * **Track ID:** The ID number of the displayed object. Can be found by checking **Show IDs?** in the [[usage: | ||
+ | * **Equate lengths?:** Select to stretch or compress object profiles to ensure that profile length is constant over time. Deselect to display object profiles at native lengths at all timepoints. | ||
+ | |||
+ | {{ : | ||
+ | |||
+ | ===== Video demonstration ===== | ||
+ | |||
+ | {{ youtube> |