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--- usage:plotting [2020/05/26 14:24] – [Plot and data selection] pseudomoaner
+++ usage:plotting [2022/09/05 23:05] (current) – pseudomoaner
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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 |}}
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 {{ :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 profile length is constant over time. Deselect to display object profiles at native lengths at all timepoints.
-{{ :usage:kymograph.png?nolink&400 |}}
 ==== Event-centred average ====
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 {{ :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 }}