anndata | Annotated data. -
kandi X-RAY | anndata Summary
kandi X-RAY | anndata Summary
Annotated data.
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Top functions reviewed by kandi - BETA
- Concatenate multiple pandas .
- Concatenate two AnnDataFrames .
- Read a Loom data file .
- Read data from file .
- Read an hdf5 file .
- Append a sparse matrix to a SparseDataset .
- Make an index unique .
- Write data to csv file .
- Return a sparse matrix representation of el .
- Decorator to deprecate positional arguments .
anndata Key Features
anndata Examples and Code Snippets
Lines of Code : 28License : Strong Copyleft (CC BY-SA 4.0)
Copy from anndata import AnnData
import numpy as np
import pandas as pd
#-- Create minimal reproducible example
gene_exp = np.array([[0,32,0,1], [1,2,1,34], [65,2,4,1]])
adata = AnnData(gene_exp)
adata.obs['annopip install python-igraph
test_df = pd.DataFrame({'1':[1600,1600,1600,1700,1800],'2':[1500,2000,1400,1500,2000],
'3':[2000,2000,2000,2000,2000],'51':[65,80,75,80,75],'52':[63,82,85,85,75],'53':
[83,80,75,76,78]})
new_df = test_df[['1', '2'In [246]: x=sparse.csr_matrix(np.eye(10))
In [247]: x[0,3]=int(4)
/usr/local/lib/python3.6/dist-px = {}
list_number = 1
for list in x1, x2, x3, x4:
for q1 in range(0, 20):
for q2 in range(0, len(list.var)):
x['x{}'.format(list_number)]['mean' + str(q1)] = np.mean(list.X[:,q2])
list_number += 1
Community Discussions
Trending Discussions on anndata
QUESTION
So, I have this document that contains a list of image path that its file have been stored inside Firebase Storage. So my problem here is, how can I use future builder to load out all the images.
I have try to display out a single file with this method and its works but I just cant connect the way to display out all the file by using Future Builder.
...ANSWER
Answered 2022-Mar-22 at 15:59As suggested by @Frank van Puffelen,If you have an array of image paths, you'll want to loop over those and generate a separate FutureBuilder for each of them.
QUESTION
Can someone help me and tell me how to split a gene into 2 genes based on the anndata.obs['sample'] values?
(https://github.com/theislab/anndata)
Because there are 2 transgenic genes and most of the sequences are the same, which can't be separated during alignment.
Those 2 genes are in different samples so I want to split them in the anndata file. Thanks a lot.
Best
...ANSWER
Answered 2021-Jul-08 at 08:17I don't know if there's a way in AnnData to do it, but we can manipulate the numpy array and pandas data frames then create a new AnnData with the added row for the new gene we added manually.
This should be a reproducible example:
QUESTION
I'm trying to edit a List (composed of mutable strings) with an edit button and a function. My code is:
...ANSWER
Answered 2021-Jan-26 at 09:34You need to delete item within a loop because your data is a two-dimensional array. Like this
QUESTION
I'm designin a View to store and show some strings written by the user, and I would like to add an edit button in the toolbar in order to eliminate only the choosen strings.
I tried adding .onDelete property with an specific function but I get the error: Value of type 'List.Index>, Range<[AnnData]>.Index>.Element, ForEach, Range.Element, Text>>>' (aka 'List>>') has no member 'onDelete'
My code is the following:
...ANSWER
Answered 2021-Jan-25 at 11:21Use inside the List. Give onDelete to ForEach. Like this
QUESTION
I want to subset anndata on basis of clusters, but i am not able to understand how to do it.
I am running scVelo pipeline, and in that i ran tl.louvain function to cluster cells on basis of louvain. I got around 32 clusters, of which cluster 2 and 4 is of my interest, and i have to run the pipeline further on these clusters only. (Initially i had the loom file which i read in scVelo, so i have now the anndata.)
I tried using adata.obs["louvain"] which gave me the cluster information, but i need to write a new anndata with only 2 clusters and process further.
Please help on how to subset anndata. Any help is highly appreciated. (Being very new to it, i am finding it difficult to get)
...ANSWER
Answered 2020-Oct-13 at 08:37If your adata.obs has a "louvain" column that I'd expect after running tl.louvain, you could do the subsetting as
adata[adata.obs["louvain"] == "2"]
if you want to obtain one cluster and
adata[adata.obs['louvain'].isin(['2', '4'])]
for obtaining cluster 2 & 4.
QUESTION
I tried running code below using scanpy library but for some reason it reports an error
...ANSWER
Answered 2020-Jan-28 at 01:06You just need to run install igraph library using the command
Community Discussions, Code Snippets contain sources that include Stack Exchange Network
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Install anndata
You can use anndata 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.
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