DOC: Add animations tutorial #547
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| .. index:: animations | ||
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| How to create an animation using Emperor |
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Is this a question or will it be better to say: "Creating an animation using Emperor"?
| category. | ||
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| To do this, we need to have two metadata categories, a *gradient* category, and | ||
| a *trajectory* category. The *gradient* category determines the order in which |
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Have we always call it trajectory? IMOO it sounds confusing cause the trajectory is given by the gradient, right? Perhaps grouping is a better name but OK if this is how we always have call it.
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I think we have always called it that, or at least that's the name given in the menu, and it's the name we used in the manuscript.
| the oral microbiome changes in a cohort of 3 mice over the course of 5 weeks, | ||
| each sample will be described by the following columns: | ||
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| * ``cage_number``: the cage where each mice was housed, more than one mice could |
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AFAIK, you don't need this for the animation, right? But perhaps I need to read further down.
| have resided in the same cage. | ||
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| * ``age_in_years``: the age of each mice in years. | ||
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I guess we are planning to describe 2 trajectories examples, not only one, right?
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| * ``week``: the number of the week in this experiment. | ||
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| * ``sex``: the sex of each mice. |
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Is this category really need it by the animation? Perhaps adding some text after the description saying why we want it will be useful.
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I've added this two paragraphs after the description of these columns.
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| * ``mice_identifier``: where each mice is assigned a unique identifier. | ||
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| In the example above, we can use the ``week`` column as our *gradient* category, |
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Which example? I think we are still in the example ... 😉
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| In the example above, we can use the ``week`` column as our *gradient* category, | ||
| so as long as all the values are numerical. To be more precise, a column where | ||
| values were indicated as ``pre-treatment, first, second, third and last`` would |
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This is super important and perhaps it should be part of the description of each category and why we want them.
| In the next section we will go through an example using published data from | ||
| `Weingarden et al. 2015 <https://www.ncbi.nlm.nih.gov/pubmed/25825673>`_. | ||
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| Data |
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Why do we need 2 examples that are different mice/human? If you want to add them both suggest splitting them clearly.
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We don't really need both, but I think that if you are unfamiliar with the topic, it may be of more help to look at a small synthetic example with just a handful of data points. As per your other comments, I've made the distinction between these two more explicit, hopefully this will help.
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@antgonza thanks for the review, I think most of your comments have been addressed, let me know if this looks better now. |
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| In this tutorial we describe how to create a principal coordinates analysis | ||
| (PCoA) plot, and display animated traces of the samples sorted by a metadata | ||
| category. To do this, we will describe a `Synthetic Example` (explaining |
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To do this -> Here | For this purpose, ... Just cause that's how the next paragraph starts.
| .. figure:: trajectories.png | ||
| :alt: Cartoon representation of the example above. | ||
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| Cartoon representation of the example we see above. On the left, the |
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we see above -> of the synthetic example
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| Cartoon representation of the example we see above. On the left, the | ||
| unmodified ordination coloring samples by mice. On the center, the same | ||
| odination with a label for each sample, corresponding to the week where this |
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| ---- | ||
| Data | ||
| ---- |
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Could you use these same divisions (data, processing, filtering) in the synthetic example? Also, could you add a small description of each section before starting the examples.
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I've now separated the sections of the two examples. The filtering section is really a "you should know" thing, not really part of the second example. I've changed the headers to make this distinction clearer.
| be logged in to access the studies. | ||
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| The files needed for this tutorial can be downloaded from this `link | ||
| <http://emperor.microbio.me/animations-tutorial.zip>`_, download and unzip in |
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I think the download and unzip is obvious but if you want to leave it change to: '. Download and unzip in'
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I've now made these changes, thanks! |
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Thanks!! Looks great. One more request, which I just thought of: how to deal with missing data? In specific, what happens if one mouse has only -1, 3? |
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@antgonza good point, I had already considered this in the red samples, but did not highlight this in the text, this has now been mentioned in the text (right after the figure). |
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Thanks @antgonza! |
This adds a tutorial on how to create animations and a brief explanation of the concepts behind them.