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Vim Cheat Sheet

Insert vs. command mode

• i: insert mode
• o: insert mode, but one line below
• esc: exit insert mode and return to command mode

Navigation

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library(dplyr)
library(readr)
library(metacoder)

# read in gdtb rs207 lineage/taxonomy information and format
# csv available here: https://osf.io/p6z3w/
gtdb_lineages <- read_csv("gtdb-rs207.taxonomy.csv.gz") %>% # read in gtdb rs207 lineage information
  mutate(full_lineage = paste(sep = ";", superkingdom, phylum, class, order, family, genus, species)) %>% # format lineage into single string
  select(ident, full_lineage) # keep columns that will be used by metacoder

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Login (requires password and duo authentication)

ssh -l <your-xsede-username> login.xsede.org
gsissh rmacc-summit
# OR to get a specific login node
gsissh login12.colorado.xsede.org

Check disk usage

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library(jsonlite)
library(dplyr)
carpentries_json <- read_json("https://feeds.carpentries.org/dc_past_workshops.json")
carpentries_df <- do.call(rbind, lapply(carpentries_json, rbind))
carpentries_df <- carpentries_df %>%
  as.data.frame() %>%
  mutate_all(as.character)

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################################################################################
## Intro to plotting with ggplot2: other goodies 2020-02-20
################################################################################


# Getting started ---------------------------------------------------------

# First let's download a data set called "portal_data_joined.csv"
# We'll put it in our data folder inside of our project directory.
# If you don't already have a data directory, you can create one in 

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Create a horizontal scroll bar for code chunks in an html doc:

```{css, echo=FALSE}
pre, code {white-space:pre !important; overflow-x:auto}
```

Change the width of a markdown figure:

![](figures/dag_quant.png){ width=30% }

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#! /usr/bin/env python

import sourmash


if __name__ == "__main__":
    import argparse

    parser = argparse.ArgumentParser()
    parser.add_argument("-k", "--ksize", type=int, default=51)

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knitr::purl(input = "/path/to/file.Rmd", "/path/to/output_script.R", documentation = 0)

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Sum over a column in a csv:

cat file.csv| cut -d "," -f 2 | paste -sd+ - | bc

Pretty view a csv in less:

cat file.csv | column -t -s, | less -S

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git checkout -b tr_sourmash_2019 origin/tr_sourmash_2019 --track