Merge pull request #34 from zktuong/devel

0.0.21

README.md

@@ -2,10 +2,10 @@
 
 ![dandelion_logo](notebooks/img/dandelion_logo.png)
 
-Version = 0.0.17
+Version = 0.0.21
 
 ## 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 of immcantation tools for single-cell BCR analysis and includes a couple of functions for visualization. 
+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. 
 
 Overview
 
@@ -26,41 +26,40 @@ I would reccomend instaling this in order:
 ```bash
 # in bash/zsh terminal
 # create a conda environment with specific modules
-conda create --name dandelion python=3.7
+conda create --name dandelion python=3.7 
 conda activate dandelion
 
-# the following two are what's required by scanpy
+# the following are normal installation intructions for scanpy
 conda install seaborn scikit-learn statsmodels numba pytables
-conda install -c conda-forge python-igraph leidenalg 
+conda install -c conda-forge python-igraph leidenalg
+pip install scanpy 
+
 # these are required by dandelion
-conda install distance scikit-bio joblib plotnine jupyter adjustText
-conda install -c bioconda igblast blast changeo presto
+conda install -c conda-forge distance joblib plotnine adjustText jupyter
+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
 # 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
 
 # Use pip to install the following with --no-cache-dir --upgrade if necessary
-pip install networkx polyleven scrublet scanpy
-
 # and then lastly install this
 pip install git+https://github.com/zktuong/dandelion.git
 
 # for the development branch, run this:
 pip install git+https://github.com/zktuong/dandelion.git@devel
 ````
 
-dandelion also requires some R packages intalled.
+`dandelion` also requires some R packages intalled.
 ```R
 # in R
 install.packages(c("optparse", "alakazam", "tigger", "airr", "shazam"))
 ```
 or the following if using conda to manage R:
 ```bash
 # in bash/zsh terminal
-conda install -c bioconda r-optparse
-conda install -c conda-forge r-alakazam r-tigger r-airr r-shazam
+conda install -c conda-forge r-optparse r-alakazam r-tigger r-airr r-shazam
 ```
 
 The package should now be properly installed and when starting up jupyter notebook in the virtual environment, the kernel `python3` should work. Otherwise, you might need to add it manually:
@@ -74,6 +73,7 @@ Last but not least, you will need to download the database folder in this reposi
 
 So for example, if I unpack into `~/Documents`
 ```bash
+# in bash/zsh terminal
 # set up environmental variables in ~/.bash_profile
 export GERMLINE=~/Documents/dandelion/database/germlines/
 export IGDATA=~/Documents/dandelion/database/igblast/
@@ -83,30 +83,28 @@ export BLASTDB=~/Documents/dandelion/database/blast/
 ## External softwares
 While blast and igblast executables are managed through conda, you can also download [igblast](https://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST/) and [blast+](https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/) manually, and store the softwares somewhere accessible. Just make sure to set the paths to them appropriately.
 ```bash
+# in bash/zsh terminal
 # unpack where relevant and export the path to the softwares, e.g. ~/Documents/
 echo 'export PATH=~/Documents/software/bin:$PATH' >> ~/.bash_profile
 source ~/.bash_profile
 ```
 
-## Requirements
+## Basic Requirements
 Python packages
 ```python
 # conda
-python==3.7.6 (conda-forge)
-numpy==1.18.4 (conda-forge)
-pandas==1.0.3 (conda-forge)
-distance==0.1.3 (conda-forge)
+python>=3.7,<3.8 (conda-forge)
+numpy>=1.18.4 (conda-forge)
+pandas>=1.0.3 (conda-forge)
+distance>=0.1.3 (conda-forge)
 joblib==0.14.1 (conda-forge)
 jupyter==1.0.0 (conda-forge)
-scikit-learn==0.23.0 (conda-forge)
-numba==0.48.0 (conda-forge)
+scikit-learn>=0.23.0 (conda-forge)
+numba>=0.48.0 (conda-forge)
 pytables==3.6.1 (conda-forge)
-seaborn==0.10.1 (conda-forge)
-leidenalg==0.8.0 (conda-forge)
-plotnine==0.6.0 (conda-forge)
-scikit-bio==0.5.6 (conda-forge)
-changeo==1.0.0 (bioconda)
-presto==0.6.0 (bioconda)
+seaborn>=0.10.1 (conda-forge)
+leidenalg>=0.8.0 (conda-forge)
+plotnine>=0.6.0 (conda-forge)
 
 # Other executables (through conda)
 blast>=2.10.0 (bioconda) # depends on the database version as well
@@ -115,7 +113,10 @@ igblast==1.15.0 (bioconda)
 # pip
 anndata>=0.7.1
 scanpy>=1.4.6
-scrublet==0.2.1
+scrublet>=0.2.1
+scikit-bio>=0.5.6 
+changeo>=1.0.0
+presto>=0.6.0
 polyleven>=0.5
 networkx>=2.4
 rpy2>=3.3.2
@@ -131,7 +132,7 @@ ggplot2
 ```
 
 ## Acknowledgements
-I would like to acknowledge the contributions from Dr. Ondrej Suschanek, Dr. Benjamin Stewart, Dr. Rachel Bashford-Rogers and Prof. Menna Clatworthy who helped with the initial conception of the project and for all discussions. 
+I would like to acknowledge the contributions from Dr. Ondrej Suschanek, Dr. Benjamin Stewart, Dr. Rachel Bashford-Rogers and Prof. Menna Clatworthy, who helped with the initial conception of the project and for all discussions. 
 
 I would also like to acknowledge Dr. Jongeun Park, Dr. Cecilia-Dominguez Conde, Dr. Hamish King, Dr. Krysztof Polanksi and Dr. Peng He with whom I have had very useful discussions. I would also like to thank my wife who helped name the package, because she thought the plots looked like a dandelion =D.
 

bin/tigger-genotype.R

@@ -61,7 +61,7 @@ opt_list <- list(make_option(c("-d", "--db"), dest="DB",
                              help=paste("Output directory. Will be created if it does not exist.",
                                         "\n\t\tDefaults to the current working directory.")),
                  make_option(c("-f", "--format"), dest="FORMAT", default=FORMAT,
-                             help=paste("File format. One of 'airr' (default) or 'changeo'.")),                 
+                             help=paste("File format. One of 'blast' (default), 'changeo' or 'airr'.")),                 
                  make_option(c("-p", "--nproc"), dest="NPROC", default=NPROC,
                              help=paste("Number of subprocesses for multiprocessing tools.",
                                         "\n\t\tDefaults to the available processing units.")))
@@ -101,7 +101,7 @@ if (opt$FORMAT == "changeo") {
     junction_length <- "junction_length"
     sequence_alignment <- "sequence_alignment"
     ext <- "tsv"
-} else if (opt$FORMAT == "airr") {
+} else if (opt$FORMAT %in% "airr") {
     db <- airr::read_rearrangement(opt$DB)
     v_call <- "v_call"
     j_call <- "j_call"

dandelion/plotting/__init__.py

@@ -2,6 +2,6 @@
 # @Author: Kelvin
 # @Date:   2020-05-13 23:21:45
 # @Last Modified by:   Kelvin
-# @Last Modified time: 2020-08-17 18:22:17
+# @Last Modified time: 2020-11-13 20:10:00
 
-from ._plotting import random_palette, clone_network, barplot, stackedbarplot, spectratype, clone_rarefaction
+from ._plotting import random_palette, clone_network, barplot, stackedbarplot, spectratype, clone_rarefaction, clone_overlap