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#!/bin/bash | |
set -eox pipefail | |
git clone https://github.com/rapidsai/rapidsai-csp-utils.git | |
bash rapidsai-csp-utils/colab/rapids-colab.sh stable |
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import numpy as np | |
import scanpy as sc | |
import anndata | |
import sys | |
import time | |
import os |
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import sys, os | |
dist_package_index = sys.path.index('/usr/local/lib/python3.6/dist-packages') | |
sys.path = sys.path[:dist_package_index] + ['/usr/local/lib/python3.6/site-packages'] + sys.path[dist_package_index:] | |
sys.path | |
exec(open('rapidsai-csp-utils/colab/update_modules.py').read(), globals()) |
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name: ribohmm | |
channels: | |
- conda-forge | |
- bioconda | |
- r | |
- defaults | |
dependencies: | |
- bcftools=1.9=h4da6232_0 | |
- htslib=1.9=hc238db4_4 | |
- libdeflate=1.0=h470a237_0 |
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barplot <- function(df, showCategory=15){ | |
df <- df[with(df, order(ratio, padj, decreasing = c(TRUE, FALSE))),] | |
df <- head(df, n=showCategory) | |
breaks <- round( c(0, 1/4, 2/4, 3/4, 1) * max(df[['ratio']]) , 2) | |
p_plot <- ggplot(df, aes_string(x="term", y="ratio", fill="padj")) + | |
geom_col() + | |
scale_y_continuous(expand=c(0, 0), breaks=breaks, limits=c(0, max(df[["ratio"]]+0.05))) + | |
scale_x_discrete(name='GO term') + | |
scale_fill_continuous(low="#00dbde", high="#FFF94C") + | |
theme(text=ggplot2::element_text(size=9)) + |
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