ANY-maze Help > The ANY-maze reference > The Protocol page > The elements of a protocol > Reports > Track plots > Setting up a Track plot > Specifying the colour, width and transparency of a track plot

Specifying the colour, width and transparency of a track plot

In brief

If you wish, ANY-maze can colour-code the track shown in a track plot so that its colour represents something - for example, how fast the animal is moving, perhaps blue for moving slowly, red for moving fast and orange for anything else - as in figure 1.

You can also specify how wide and how transparent the track should be.

Figure 1. A track plot in which the track has been colour-coded to show how fast the animal is moving.

Details

Choosing what to base the track colour on

There are lots of things that can be used to colour-code the track including:

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The time segment of the test

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The time period of the test

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The zone the animal is in

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Whether a behaviour being scored using a key is occurring

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Whether an on/off input, such as a photo-beam is active

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Whether a binary output, such as a speaker, a shocker or a laser, controller is active

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Whether a virtual switch is active.

This last option (whether a virtual switch is active) can be extremely useful, and is how you could colour-code the track depending on how fast the animal is moving. This is because a virtual switch can be set to switch on when some value goes above or below a threshold - in this case the animal's speed going above a 'moving fast' threshold. You'll find all the details here.

Note that you can't colour-code the track based on multiple different things; so while, for example, you could colour-code the track to show when an optogenetic laser was on, you couldn't also colour-code it to show when the animal is moving fast - you could only do one or the other. Of course, you could create two track plots, one showing the laser and the other the animal's speed.

Setting the colour-coding

To actually set a the colour-coding you simply need to select the appropriate group, such as Colour-code the track based on segment of test and then choose which specific items you want to include, so this might just be the first 30 seconds of the test. You can then choose the colour you want the track to be shown in. Any part of the track which doesn't fall within the colour-coding (so in this example that would be all the track after the first 30s of the test) will be shown in the default track colour - see figure 2.

Figure 2. Setting track colour-coding is as simple as selecting what causes the track to change colour and then specifying the colour to use.

Some points to note

The colour of the track changes at exactly the time when the thing it is showing changes. For example if the track is to show the first 30s of the test in blue and rest in red, then at exactly 30.000s the track will change from blue to red. This might seem rather obvious, but remember ANY-maze only detects the animal in the images sent from the camera which typically means 30 times per second, and even then, it may not record every position. So what if it knows where the animal was at time 29.900s and at time 30.250s but not at 30.000s? The answer is that it will use linear interpolation to estimate where the animal would have been at time 30.000s (i.e. how far along a straight line between its position at time 29.900 and 30.250) and change the colour of the track at that point.

There is one situation where the colour-coding can appear a little odd, which is where the colour of the track is based on the zone the animal is in. Consider the situation in which at time 1.000s the animal is at a coordinate of 100,100 and that the next position we have is at time 2.000s when the animal is at a coordinate of 200,100.

Now imagine that there's a border between zone A and zone B at 150,100, - so the animal will have moved from zone A to zone B - but what colour should the track be between the position at time 1.000s, in zone A, and the position at time 2.000s in zone B? An obvious answer would be to draw it partly in the colour for zone A and partly in the colour for zone B (like the situation described above where the track was colour-coded based on time). However, this situation is a little different; in the case of the time we knew the track should change colour at time 30.000s, but in this case we only know that at time 1.000s the animal wasn't in zone B and at time 2.000s it was, we don't know when it entered the zone.

This is a common situation throughout ANY-maze and the program always deals with it by assuming the animal is in a zone until it knows it isn't. Another way of looking at this is that time (and distance) are always attributed to the zone the animal is leaving. So in this example, we'd would say the for the time from 1.000s to 2.000s the animal was in zone A. Then, from time 2.000s onwards we consider it to be in zone B, because that's when we know it's in the zone. This rule applies everywhere in ANY-maze and track plots are no different, so what this means is that the track from 100,100 (in zone A) will ALL be drawn in the 'zone A' colour right up to the point 200,100 (which is in zone B), in other words some of the track will be in zone B but drawn in the colour of zone A.

Setting the track width and transparency

The width of the track can be set any value from 1 (very thin) to 20 (chunky).

The track's transparency can be set to any value from 0% (opaque) to 99% (almost entirely transparent). The transparency is particularly relevant when the track is plotted over a background image or heat map, or when it includes markers, although it can also be used to make the plot clearer where the tracks overlap.

ANY-maze help topic T0682