snipets

code snipets with tricks and reusable components I find handly and helpful. Please feel free to contribute any code snippets that you find helpful.

Subject specific code snippets are available in the individual pages.

R

Python

Bioinformatics (mix of R and Python snippets)

A few examples are listed here.

Reading sparse matrix in python

from scipy import io
counts = io.mmread('matrix.mtx.gz')
counts.toarray()

Tags : cellranger , count matrix, read sparse matrix

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Getting HEX values from ggplot2 color hue - R code

a <- scale_color_hue(h.start=180)
a$palette(7)#number of colors

This is helpful, especially if you are using both R and Python(or anythong else) and wanted to have plots have same color representation.

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Exporting Seurat object from R to scanpy readable object

First export the Seurat object as h5ad format using R

library(Seurat)
library(SeuratData)
library(SeuratDisk)
library(reticulate)

libd.151507 <- readRDS("data/processed_data/151507.rds")#reading seurat object processed and stored in directory

SaveH5Seurat(libd.151507, filename = "data/processed_data/libd.151507.h5Seurat")
Convert("data/processed_data/libd.151507.h5Seurat", dest = "data/processed_data/libd.151507.h5ad")

Then, import the h5ad object using scanpy in Python

import pandas as pd
import numpy as np
import sys
from anndata import AnnData
import scanpy as sc

adata = sc.read_h5ad("data/processed_data/libd.151507.h5ad")