I'm using MATLAB to generate 'phytrees' and I need to simplify them.
The way I thought is by removing subtrees where all the node has the same value and keep only this value + a number that represent how many nodes were deleted.
For example, here is one of the trees:
and I want to replace the subtrees that have the same values like here:
Is there a way to do so?
I did not find a programmatic way to do it, but from the picture you attached I see that you use plot to view your figure. If instead, you'll use the phytreeviewer (just type view(your_phylotree)) you'll get a different figure window, with other related tools.
Specifically, you'll see the Collapse branch button , and the Rename branch button , which will together get you exactly what you want. The first "removing subtrees" (actually hiding them), and the second lets you change the branch name to "value + a number".
You can do all this also by simply right-clicking in the relevant brunch:
Here is an example with data from the docs:
% bulding some tree:
seqs = fastaread('pf00002.fa');
distances = seqpdist(seqs,'method','jukes-cantor','indels','pair');
phylotree = seqneighjoin(distances,'equivar',seqs);
view(phylotree)
After some collapsing and renaming on this tree, and printing it to a figure (with right click on the most top branch, or the root, that you want to include in the figure), I got:
Also, note that every time you hover with the mouse on a branch (even if collapsed) you get a list of the Leafs in that branch and their count:
Related
How can I display one dataseries as bar and another as a line in one graph like it is used in the last comment of: see last picture
Short answer:
It's not possible (yet) using the Grafana UI, only by hand.
Long answer:
As far as I know there is no way of doing this using the UI switches; you'll have to use the use the "alias or regex" fields below the visualisation configuration.
Prepare your data
Before you start, make sure that your queries A and B retrieve actual data. You won't see your data otherwise and be confused why they're not showing.
Adding fields and values to the aliases
Once you are selecting the correct data you want to display, just add the following on the visualisation section of the graph at the 'alias or regex' fields:
Add 2 overrides, one for each value you want to display using the 'Add series override' button.
Add a "Bars:false" option flag and a "Lines:true" for the value you want as a line.
Be sure to use the exact opposite values for your bars ("Bars:true" & "Lines:false")
Add a 'Y-axis: 2' to the value you want to have on the right side of your graph.
Optionally, you can add a "Z-index: 3" for the value that you want to have on top (I added this option to the line to make sure it's always drawing on top of the bars).
Enjoy
You should now have a nice graph with 2 types of data and visualisations in one; something like this:
For those who were asking in the comment section, yes this isn't available in version 8, however, you can still change the time series visualization to graph(old) so you can set the alias/regex.
I have a table which consists of 17025 rows. When I try to display the table, the whole table displays. But I want it in small parts. How do I make it display in small parts.
Type more on at the MATLAB command prompt. Subsequent output will be paused after every screenful.
Documentation: https://www.mathworks.com/help/matlab/ref/more.html
I usually check my variables in these ways:
Suppose that we have a variable called A=rand(1000,1000).
1.we can display a part of A by calling A(127:130,241:243), to show the specific part of it.
>> A(127:130,241:243)
ans =
0.8152 0.0674 0.5609
0.1977 0.3906 0.6491
0.3288 0.1255 0.7478
0.9176 0.4253 0.5111
2.double click the name of the variable in the Workspace, so we could check it in Variables.
3.if your data only contain few columns, I recommend you to draw them in a figure and view them by dragging a Data Cursor in the picture.
SampleCode:
A=[1:1:200; 250:-1:51];
plot(A')
However, only the first option could display matrix on command window, but 2&3 is much faster since we don't know which part to display.
I have built a bokeh app that allows users to select windows in data and run python code to find and label (with markers) extreme values within these limits. For ease of interaction, I use the box select tool for the range selection. My problem arises when repeating this process for subsequent cases. After markers are placed for the results, they are rendered invisible by setting alpha to zero and another case needs to be chosen. When the new select box includes previous markers, they become visible based on the selection. How do I override this default behavior? Can markers be made unselectable? or can I add code to the customJS to hide them after they are selected?
Thanks in advance for any help!
There are a few possible approaches. If you just want non-selected glyphs to "disappear" visually, you can set a policy to do that as described here:
http://docs.bokeh.org/en/latest/docs/user_guide/styling.html#selected-and-unselected-glyphs
Basically, for bokeh.plotting, pass
nonselection_fill_alpha=0.0,
nonselection_line_alpha=0.0,
as arguments to your plot.circle call or whatever. Or if you are using the low level bokeh.models interface, something like:
renderer.nonselection_glyph = Circle(fill_alpha=0.0, line_alpha=0.0)
But be aware (I think you already are) that the invisible markers are still there, and still selectable if the user happens to draw a box over them with the selection tool.
If you truly want only a subset of the data to be visible and selectable after a selection, I'd say you want to replace the data in the column data source wholesale with the subset in your selection callback.
I was wondering if someone could explain to me how I update a list at runtime in Unity?
For example I have a spell book, which has 3 spells in it, when I drag them to my action bar they get re-parented to it, what I'm trying to do is get a list of each child under the actionbar transform,
My problem is where to actually do something like this if I try something like below in the update, it adds whatever's there many times, which I can understand since update runs every frame..
list = actionbarui.GetComponent(UIGrid).GetChildList();
for(var i =0;i < list.size; i++)
{
buttonList.Add(list[i].gameObject);
}
If I add a callback to the buttons so that whenever they're drag and dropped it runs the above code and add thing's additively, as in, if you drag just one "spell" on it will loop through once, which is fine, but as soon as you add another it loops through three times, that is, it already has one it then adds the same one again PLUS the new button that's just been dragged on for a total of 3.
I've tried changing the code to
list = actionbarui.GetComponent(UIGrid).GetChildList();
for each(var child : Transform in list.GetEnumerator())
{
buttonList.Add(child.gameObject);
}
But this simple doesn't add anything, I am unsure how to go about keep the lists update as they are dragged off and on, could anyone please explain how this is achieved?
Please ignore the second "list" code, it's implementing "BetterLists" as apart of NGUI, so doesn't follow standard list methods.
Thank you for reading
If I add a callback to the buttons so that whenever they're drag and dropped it runs the above code and add thing's additively, as in, if you drag just one "spell" on it will loop through once, which is fine, but as soon as you add another it loops through three times, that is, it already has one it then adds the same one again PLUS the new button that's just been dragged on for a total of 3.
That is the expected result here. You are running through the list of children and adding them to your buttonlist, so first time there is only one item to add, then when you add another child there are two items to add, thus resulting in three items.
Either don't have a for loop and do:
buttonList.Add(the_GameObject_that_was_just_added_to_the_bar);
Or clear your buttonList before the for loop:
list = actionbarui.GetComponent(UIGrid).GetChildList();
buttonList.Clear();
for(var i =0;i < list.size; i++)
{
buttonList.Add(list[i].gameObject);
}
Alternatively to Dover8's response, you can first check if the buttonList already contains a reference to the child to be added. If it does, continue. Otherwise add the new child.
However, given the expense of doing the checks, and since you are already looping through the list already, I'd recommend that you follow his suggestion to clear the list before running the loop. It will probably give you the best performance out of these examples.
If there's a reason you can't or shouldn't clear the buttonList, and you still need to run through it, I'd recommend my suggestion. It really depends on which implementation works best for what you are trying to do. The point is that there are several ways to do this, and they have different performance profiles you need to consider.
I've been learning more about the d3 visualization library, and I've seen a few examples of bar charts that have a snippet that looks like
chart.selectAll("rect")
.data(data)
.enter().append("rect")
.attr("y", y)
.attr("width", x)
.attr("height", y.rangeBand());
My confusion is with the first selectAll line. What is the purpose of selecting all rects before they exist since we'll be appending new rects on data enter? Does what goes in the selectAll matter if none of those elements exist?
It is part of the declarative nature of the D3 language. The Thinking with Joins article explains it in detail. An excerpt:
But what’s with the selectAll("circle")? Why do you have to select
elements that don’t exist in order to create new ones? WAT.
Here’s the deal: instead of telling D3 how to do something, tell D3
what you want. In this case, you want the circle elements to
correspond to data: you want one circle per datum. Instead of
instructing D3 to create circles, then, tell D3 that the selection
"circle" should correspond to data—and describe how to get there. This
concept is called the data-join:
This Venn diagram illustrates the data-join. Data bound to existing
elements produce the update (inner) selection. Unbound data produce
the enter selection (left), and unbound elements produce the exit
selection (right). Data Enter Update Elements Exit Thinking with joins
reveals the mystery behind the sequence:
The selectAll("circle") returns the empty selection, since the SVG
container element (svg) is empty. No magic here.
The empty selection is joined to data: data(data). The data method
binds data to elements, producing three virtual selections: enter,
update and exit. The enter selection contains placeholders for any
missing elements. The update selection contains existing elements,
bound to data. Any remaining elements end up in the exit selection for
removal.
Since the selection was empty, all data ends up as placeholder nodes
in enter().
This is the same append as in the first example, but applied to
multiple placeholders; selection methods implicitly iterate over
selected elements. The missing elements are added to the SVG container
by append("circle").
So that’s it. You wanted the selection "circle" to correspond to data,
and you described how to create the missing elements.
In your example selectAll("rect") is called first. But it returns an empty selection.
data(data) will bind the empty selection with the data. It creates new empty selections.
.enter() identifies any DOM elements that needs to be added when the joined array is longer than the selection.
append("rect") appends a rectangle to each empty selection, which is no longer empty
It is well explained and detailed on this section: D3.js data binding, How it works?