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usage:plotting [2019/07/19 16:31] – [The Plotting module] pseudomoaner | usage:plotting [2022/09/05 23:05] (current) – pseudomoaner | ||
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- | With the plotting module, you can explore your track data through a simple, user-friendly interface. As well as those tools available by default, the plotting module also supports certain types of user-defined data, described in the [[usage: | + | With the plotting module, you can explore your track data through a simple, user-friendly interface. As well as those tools available by default, the plotting module also supports certain types of user-defined data, described in the [[usage: |
+ | |||
+ | Plots generated through the plotting module can also be exported in a variety of formats, each providing different degrees of flexibility and ease of use. At its most powerful, analysed data can be exported and combined externally with other datasets to generate publication-quality plots. | ||
===== Plot and data selection ===== | ===== Plot and data selection ===== | ||
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<note tip> | <note tip> | ||
- | 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 most flexible option is the **Export figure data** option. Data associated with the currently visible axes will be saved in the root directory, under the name ' | The most flexible option is the **Export figure data** option. Data associated with the currently visible axes will be saved in the root directory, under the name ' | ||
- | 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) | + | 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) |
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+ | 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 in the main GUI however, the **times** and **dataMeans** fields of plotExport will be replaced with **subTimes** and **subData**, | ||
=== 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' | ||
{{ : | {{ : | ||
==== 2D histogram ==== | ==== 2D histogram ==== | ||
- | Generates a heatmap of the bivariate distribution between the two indicated track-associated datasets. Similar to **Joint distribution**, | + | Generates a heatmap of the bivariate distribution between the two indicated track-associated datasets. Similar to **Joint distribution**, |
Options: | Options: | ||
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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. | + | {{ :usage:growthcurves.png?nolink& |
- | + | ||
- | 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. | + | |
- | 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> |