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--- usage:plotting [2019/07/19 16:38] – [The Plotting module] pseudomoaner
+++ usage:plotting [2022/09/05 23:05] (current) – pseudomoaner
@@ Line 19: / Line 19: @@
 <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's angular velocity as a new field can be found here FIXME.
+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 each objects orientation orientation data so that it changes smoothly and saves it in the new field 'fullPhi' can be found [[post:lienarlisephi.m|here]].
 </note>
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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 'plotDataExport.mat'. This file contains two variables: **plotSettings**, a list of settings associated with the plotting module at the time the plot was exported, and **plotExport**.
-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) is stored in cells 2, 3 and 4, respectively. The structures stored within each of these cells FIXME
+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 in the main GUI however, the **times** and **dataMeans** fields of plotExport will be replaced with **subTimes** and **subData**, indicating the sampling times and values of each track separately.
 === 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.
 ==== Histograms ====
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   * **Show correlation coefficient:** Display Pearson's correlation coefficient and associated p-value for selected populations and datasets. Results are shown in top left hand corner of plot.
   * **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' option.
 {{ :usage:plotting:joint.png?nolink&600 |}}
 ==== 2D histogram ====
-Generates a heatmap of the bivariate distribution between the two indicated track-associated datasets. Similar to **Joint distribution**, but designed for higher-volume datasets.
+Generates a heatmap of the bivariate distribution between the two indicated track-associated datasets. Similar to **Joint distribution**, but designed for larger datasets.
 Options:
@@ Line 111: / Line 113: @@
 {{ :usage:plotting:2dhist.png?nolink&600 |}}
-==== Cartouche ====
-Generates a 'cartouche' by cutting out objects from each timepoint in each image channel and displaying them side by side.
+==== Phase space ====
-Options:
+Plots tracks, using arbitrary track-associated variables in place of object position as the axes. Colours track segments according to their time relative to the start of the track, early segments being shaded dark and later segments being shaded light.
-  * **Track ID:** The ID number of the displayed object. Can be found by checking **Show IDs?** in the [[usage:overlays|overlays module]].
-  * **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.
-{{ :usage:plotting:cartouche.png?nolink&600 |}}
+This plotting option is similar to the joint distribution and the 2D histogram options. It differs from the joint distribution in that all sampling points in the track are shown, rather than just the track-wide average. It differs from the 2D histogram in that points from a single track are joined together, rather than simply being binned with points from all other tracks.
-==== Kymograph ====
-Generates a kymograph (space-time plot) of the selected object in all available channels.
+{{ :usage:growthcurves.png?nolink&600 |}}
-Options:
-  * **Track ID:** The ID number of the displayed object. Can be found by checking **Show IDs?** in the [[usage:overlays|overlays module]].
-  * **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 ====
@@ Line 150: / Line 141: @@
 {{ :usage:plotting:divcentredavg.png?nolink&600 |}}
+==== Cartouche ====
+Generates a 'cartouche' by cutting out objects from each timepoint in each image channel and displaying them side by side.
+Options:
+  * **Track ID:** The ID number of the displayed object. Can be found by checking **Show IDs?** in the [[usage:overlays|overlays module]].
+  * **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.
+{{ :usage:plotting:cartouche.png?nolink&600 |}}
+==== 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:overlays|overlays module]].
+  * **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.
+{{ :usage:kymograph.png?nolink&400 |}}
+===== Video demonstration =====
+{{ youtube>yDAtP2t15S8?large }}