Merge pull request #42 from zktuong/devel

v0.0.26

last PR for the year maybe?

.gitignore

@@ -6,3 +6,10 @@
 */*/*/__pycache__/
 */*/__pycache__/
 */__pycache__/
+dist/sc-dandelion-0.0.26.tar.gz
+sc_dandelion.egg-info/dependency_links.txt
+sc_dandelion.egg-info/not-zip-safe
+sc_dandelion.egg-info/PKG-INFO
+sc_dandelion.egg-info/requires.txt
+sc_dandelion.egg-info/SOURCES.txt
+sc_dandelion.egg-info/top_level.txt

README.md

@@ -2,7 +2,7 @@
 
 ![dandelion_logo](notebooks/img/dandelion_logo.png)
 
-Version = 0.0.25
+Version = 0.0.26
 
 ## Intro
 Hi there! I have put together a python package for analyzing single cell BCR/V(D)J data from 10x Genomics 5' solution! It streamlines the pre-processing, leveraging some tools from immcantation suite, and integrates with scanpy/anndata for single-cell BCR analysis. It also includes a couple of functions for visualization. 
@@ -36,11 +36,11 @@ First, install [scanpy](https://scanpy.readthedocs.io/en/latest/installation.htm
 # these are required by dandelion
 conda install -c conda-forge distance joblib plotnine adjustText
 conda install -c bioconda igblast blast # if this doesn't work, download them manually (see below)
-conda install -c conda-forge rpy2
-# or pip install rpy2
+conda install -c conda-forge "rpy2>=3.3.2,<3.3.5" # to make compatible for R version 4
+# or pip install "rpy2>=3.3.2,<3.3.5"
 # If it fails because it's compiling using clang, first, work out where the path is to your gcc compiler (use brew to install gcc if needed):
 # then run
-# env CC=/path/to/location/of/bin/gcc-9 pip install rpy2
+# env CC=/path/to/location/of/bin/gcc-9 pip install "rpy2>=3.3.2,<3.3.5"
 
 # Use pip to install the following with --no-cache-dir --upgrade if necessary
 # and then lastly install this
@@ -68,7 +68,7 @@ python -m ipykernel install --user --name dandelion --display-name "Python (dand
 ```
 
 ## Required database
-Last but not least, you will need to download the database folder in this repository and place them somewhere accessible. The igblast and germline database folders were originally downloaded with immcantation's docker image (4.1.0) (https://immcantation.readthedocs.io/en/4.1.0/docker/intro.html). The blast database were downloaded from IMGT manually curated. I have uploaded a copy of the required databases in a separate [repository](https://github.com/zktuong/databases_for_vdj)(Last update: 28/11/2020). Once you've unpacked the folders, export the the path to the database folders as environmental variables in your `~/.bash_profile` or `~/.zshenv` like below. This will allow dandelion to access them easily. In the future, the databases will have to be updated accordingly.
+Last but not least, you will need to download the database folder in this repository and place them somewhere accessible. The igblast and germline database folders were originally downloaded with immcantation's docker image (4.1.0) (https://immcantation.readthedocs.io/en/4.1.0/docker/intro.html). The blast database were downloaded from IMGT and manually curated. I have uploaded a copy of the required databases in a separate [repository](https://github.com/zktuong/databases_for_vdj)(Last update: 28/11/2020). Once you've unpacked the folders, export the the path to the database folders as environmental variables in your `~/.bash_profile` or `~/.zshenv` like below. This will allow dandelion to access them easily. In the future, the databases will have to be updated accordingly.
 
 So for example, if I unpack into `~/Documents`
 ```bash
@@ -119,7 +119,7 @@ changeo>=1.0.0
 presto>=0.6.0
 polyleven>=0.5
 networkx>=2.4
-rpy2>=3.3.2
+rpy2>=3.3.2,<3.3.5
 ```
 
 R packages

dandelion/plotting/_plotting.py

@@ -2,7 +2,7 @@
 # @Author: Kelvin
 # @Date:   2020-05-18 00:15:00
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2020-12-13 20:47:47
+# @Last Modified time: 2020-12-16 22:29:11
 
 import seaborn as sns
 import pandas as pd
@@ -16,6 +16,7 @@
 from adjustText import adjust_text
 from plotnine import ggplot, theme_classic, aes, geom_line, xlab, ylab, options, ggtitle, labs, scale_color_manual
 from scanpy.plotting import palettes
+from time import sleep
 import matplotlib.pyplot as plt
 from itertools import combinations
 
@@ -60,6 +61,7 @@ def clone_rarefaction(self, groupby, clone_key=None, palette=None, figsize=(6,4)
     # remove those with no counts
     rowsum = res_.sum(axis = 1)
     print('removing due to zero counts:', ', '.join([res_.index[i] for i, x in enumerate(res_.sum(axis = 1) == 0) if x]))
+    sleep(0.5)
     res_ = res_[~(res_.sum(axis = 1) == 0)]
 
     # set up for calculating rarefaction

dandelion/tools/__init__.py

@@ -2,7 +2,7 @@
 # @Author: Kelvin
 # @Date:   2020-05-13 23:21:45
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2020-11-18 19:54:50
+# @Last Modified time: 2020-12-17 13:00:55
 
 from ._tools import find_clones, transfer, define_clones, clone_size, clone_overlap
 from ._network import extract_edge_weights, clone_degree, clone_centrality, generate_network