kandi X-RAY | umap Summary
kandi X-RAY | umap Summary
umap
Support
Quality
Security
License
Reuse
Top functions reviewed by kandi - BETA
- Write a set of BED files
- Generate a BED6 file
- Convert a histogram array to a multi - read mappability date
- Load a uintar array from a file
- Write the kmer to a single region
- Return the number of steps in the top 10
- Writes kmers to out_link
- Generate a sequence AR array from a chromosome
- Convert bowtie to unique ARM
- Retrieve the positions mapped to a single chromosome
- Returns a subset of a list
- Returns the name of the other chr chr
- Annotate a bed file with mapped coordinates
- Calculate mappability Mappability
- Write a multiread
- Get the AR matrix of a given chromosome
- Argument parser
- Write a UUID to a wig file
- Execute bowtie command
- Extract an array from a uint file
- Reads a BEDAR file
- Compares two bedGraphs for comparison
- Read wig value from a wig file
- Write a BED file to a BED file
- Get a dictionary of chromosome sizes
- Check that the given index exists
umap Key Features
umap Examples and Code Snippets
Community Discussions
Trending Discussions on umap
QUESTION
I've been trying to run RAPIDS on Google Colab pro, and have successfully installed the cuml and cudf packages, however I am unable to run even the example scripts.
TLDR;Anytime I try to run the fit function for cuml on Google Colab I get the following error. I get this when using the demo examples both for installation and then for cuml. This happens for a range of cuml examples (I first hit this trying to run UMAP).
...ANSWER
Answered 2021-May-06 at 17:13Colab retains cupy==7.4.0
despite conda installing cupy==8.6.0
during the RAPIDS install. It is a custom install. I just had success pip installing cupy-cuda110==8.6.0
BEFORE installing RAPIDS, with
!pip install cupy-cuda110==8.6.0
:
I'll be updating the script soon so that you won't have to do it manually, but want to test a few more things out. Thanks again for letting us know!
EDIT: script updated.
QUESTION
I have an unordered_map pointer in a structure since I need it in shared memory to access and modify as the program runs.
...ANSWER
Answered 2021-Apr-03 at 04:37Applying []
to a pointer does pointer arithmetic. You want to apply the []
to the pointed at object, so you need to explicitly dereference the pointer:
QUESTION
When training the Top2Vec model in Python 3.9.2 I get the following error:
...ANSWER
Answered 2021-Mar-31 at 18:13I'm unfamiliar with the Top2Vec
class you're using.
However, that error would be expected if code that was written to use certain properties/methods in gensim-3.8.3
hasn't been adapted for the recently-released gensim-4.0.0
, which has removed and renamed some functions for consistency.
Specifically, the vectors_docs
property has been removed. (Also, the vectors_docs_norms
property mentioned a couple lines above in an unexecuted branch.)
The small changes required in the calling code are covered in the Migrating from Gensim 3.x to 4 wiki page, which I've just updated to ensure it mentions vectors_docs
specifically.
If you don't feel comfortable appkying this & any other changes to your Top2Vec
code yourself, you may just want to report the issue to its author/maintainer, and as a temporary workaround, explicitly install the older Gensim for now. With the usual pip
-based install, you could specify an older version with:
QUESTION
I'm creating a interactive map of my campus, the ideia is to replicate what I did on uMaps, in this link. The geojson was downloaded from UMap and I'm using the coordinates that came with it.
My first issue is my coordinates in the json, originally were a GeoJson, are sorted wrongly, my long came first then lat, thus when parse Google Maps can't read properly.
Json:
...ANSWER
Answered 2021-Mar-23 at 22:19flip the coordinates lines
For clarity and ease of testing, let's define a helper function:
QUESTION
I tried installing the Scanpy package on Jupyter with "pip install Scanpy" but I got the the errors below;
ERROR: pynndescent 0.5.2 has requirement numba>=0.51.2, but you'll have numba 0.48.0 which is incompatible. ERROR: umap-learn 0.5.1 has requirement numba>=0.49, but you'll have numba 0.48.0 which is incompatible
When I tried to separately install an upgraded version of numba, I got the error below;
ERROR: Cannot uninstall 'llvmlite'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
...ANSWER
Answered 2021-Mar-21 at 14:40you can try install with pip install -c numba numba=0.51.2.1rc1 if it doesn't work for you alternativly install RUN pip install llvmlite --ignore installed before pip install numba. HAVE A GOOD DAY:)
QUESTION
I have been trying to upgrade a package based off of the most recent changes on git but the changes aren't taking effect. I ran several variations of this command, such as also using python -m pip
and the actual path to the pip version in anaconda, as well as adding --upgrade: pip install git+git://github.com/lmcinnes/umap@master
Here is the output each time:
...ANSWER
Answered 2021-Mar-17 at 09:06try using the --update
and --force-reinstall
options of pip
, or:
pip install --update --force-reinstall git+git://github.com/lcminnes/umap@master
QUESTION
I am trying to see how some known labels explain, or are adjusted to the 2D representation from my data that I get from UMAP.
I tried to use silhouette
function but the cluster information must be provided as a numeric vector and then these are the one that plot(sil)
shows. Is there a way to use the cluster names or at least show these in the plot instead of the numbers?
(similar question as here but instead of the sample labels I want to change the cluster labels)
For example:
...ANSWER
Answered 2021-Feb-17 at 14:20I figured out this can be done using factoextra
package. But it would be nice if anyone finds the way to do it with the regular plot()
function though
QUESTION
I experienced the following:
...ANSWER
Answered 2021-Mar-10 at 17:00A pattern rule is a template that tells make how to build a target. It doesn't provide make with a list of targets to build: it's just a recipe for building targets. So this pattern rule:
QUESTION
I've got a package which I've previously successfully built on ReadTheDocs, but this is no longer the case. My imports are as follows:
...ANSWER
Answered 2021-Jan-25 at 13:26Based on feedback from a helpful user, I eventually arrived at a less hack'y solution. Unfortunately, the discussion went AWOL because of an unhelpful user, who responded with pip install -U numpy
, waited for me to figure it out, edited their answer and requested I accept it. Upon being denied, the answer and comment thread vanished. I don't even remember your name, helpful user, so I can't credit you for the tip.
Apparently ReadTheDocs uses an old pip, and requiring pip>=19.0
makes scikit-learn not install from source. As such, I added that line to docs/requirements.txt
, which I had previously set up to be a ReadTheDocs requirement file. This resulted in some progress - now rather than scikit-learn complaining about numpy, it was numba. Still, some synapses connected, and I just handled any dependency problems that arose via docs/requirements.txt
, the final contents of which are:
QUESTION
i am making some callback system and i wonder if i can reserve function reference to unordered_map
so that i can invoke it later.
ANSWER
Answered 2021-Jan-19 at 20:19Regardless of wether this is something you should be doing or not (the comments under your question are covering this already), it's still worth answering your question as is.
The []
operator of map types is a veritable swiss army knife. You can do a lot of things with it.
- You can assign a value.
- You can lookup the value.
- You can lookup a value even if it doesn't exist yet.
Because of this, using that operator imposes some requirements for whatever type is stored in the map. In this specific case, you are running into the requirement that it has to be value-initializable, which references cannot be.
This applies to regular references as well by the way, not just function references.
So the answer is: You can store references in a map as much as you like as long as you don't use any function of the map that requires the reference to do something it's not allowed to.
In this case, you can use umap.at(0)(10.1);
. One of the big differences between []
and at()
is that if the key is not set yet, at()
will throw an exception instead of creating a value-initialized value.
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
Vulnerabilities
No vulnerabilities reported
Install umap
You can use umap like any standard Python library. You will need to make sure that you have a development environment consisting of a Python distribution including header files, a compiler, pip, and git installed. Make sure that your pip, setuptools, and wheel are up to date. When using pip it is generally recommended to install packages in a virtual environment to avoid changes to the system.
Support
Reuse Trending Solutions
Find, review, and download reusable Libraries, Code Snippets, Cloud APIs from over 650 million Knowledge Items
Find more librariesStay Updated
Subscribe to our newsletter for trending solutions and developer bootcamps
Share this Page