gregjohnso

#install ubuntu things
sudo apt-get update -y
sudo apt-get upgrade -y
sudo apt-get install -y build-essential libfreetype6-dev libxft-dev libncurses-dev libopenblas-dev gfortran libblas-dev liblapack-dev libatlas-base-dev linux-headers-generic linux-image-extra-virtual unzip unzip wget pkg-config zip g++ zlib1g-dev libcurl3-dev
sudo apt-get install -y vim

sudo apt-get install nvidia-375
# wget http://us.download.nvidia.com/XFree86/Linux-x86_64/375.39/NVIDIA-Linux-x86_64-375.39.run
# sudo chmod ugo+rwx NVIDIA-Linux-x86_64-375.39.run
# sudo ./NVIDIA-Linux-x86_64-375.39.run -a

gregjohnso

Port forwarding using ProxyJump and ssh tunnels

• set up a new host in your ~/.ssh/config file (change rorydm to your own username):

Host tartarus
    HostName n70
    ProxyJump qmaster
    User rorydm
    LocalForward 9999 localhost:9999

gregjohnso

function [ cumLatent, score ] = plotPCA3D(data, labels, project, cm_handle)
%Z-scores and plots the first 3 prinicple componenets
  
%gregory johnson
%gregjohnso@gmail.com


    
    if ~exist('project', 'var') | isempty(project)
        project = false;

gregjohnso

from anndata._io import h5ad
import h5py
import pandas as pd

def read_obs(hdf5_path: str) -> pd.DataFrame:
  hdf5_file = h5py.File(hdf5_path, 'r')
  df_obs = h5ad.read_dataframe(hdf5_file['obs'])
  return df_obs

df = read_obs(hdf5_path = "/my/andata/path/file.h5ad")

gregjohnso

"""From: https://github.com/scverse/scanpy/issues/1508#issuecomment-734657400"""
from matplotlib import pyplot as plt

with plt.rc_context():  # Use this to set figure params like size and dpi
    sc.pl.plotting_function(..., show=False)
    plt.savefig("path/to/file.extension", bbox_inches="tight")