fortune9

Data

Papers

• Molecular and spatial signatures of mouse brain aging at single-cell resolution
  • species: mouse
  • tissue: brain
  • https://doi.org/10.1016/j.cell.2022.12.010
• Recurrent repeat expansions in human cancer genomes. Nature 613, 96–102 (2023)

• species: human

fortune9

# The problem: Plotting from R to PNG requires that you specify x and y
# dimensions, which therefore also fixes the aspect ratio of
# the whole image. In most of my plots, I want a fixed *panel* aspect ratio, 
# but the overall dimensions of the full *plot* still depend on the dimensions 
# of other plot elements: axes, legends, titles, etc.
# In a facetted ggplot, this gets even trickier: "OK, three panels, each
# with aspect ratio of 1.5, that adds up to... wait, will every panel
# have its own y-axis, or just the leftmost one?"

# ggplot apparently computes absolute dimensions for everything EXCEPT 

fortune9

When R is started, it reads a series of files to initialize the computing environment.

Config files to read

The files are read in the following order:

1. .Renviron: hosting environment variables in the format <var>=<value>. R searches the first .Renviron file in the following order: (i) Sys.getenv("R_ENVIRON_USER"), (ii) ./.Renviron, and (iii) ~/.Renviron. Once the first .Renviron is found, others will be ignored.

fortune9

---
title: "A summary of Rmarkdown tips"
---

## Math mode

1. Add space in the expression, use '\~'. For example:

```{r}
    $This~is~an~expression~in~math~mode$

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---
title: "Notes on NextFlow"
author: "Zhenguo Zhang"
date: "`r format(Sys.time(), '%B %d, %Y')`"
output:
  github_document:
    toc: true
  html_document:
    toc: yes
    toc_float: true

fortune9

The first gist in my github

This is simply a file to start my github gist journey. This is a markdown file and you can view it in text editor, github, or convert to different formats using pandoc.

We are all set, let's go.

fortune9

#!/bin/sh

#
# a simple way to parse shell script arguments
# 
# please edit and use to your hearts content
# 


ENVIRONMENT="dev"

fortune9

People

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