chasemc

assembly_summary_refseq <- readr::read_delim("https://ftp.ncbi.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt", quote='', skip = 2, delim = "\t", col_names = c("assembly_accession", "bioproject", "biosample", "wgs_master", "refseq_category", "taxid", "species_taxid", "organism_name", "infraspecific_name", "isolate", "version_status", "assembly_level", "release_type", "genome_rep", "seq_rel_date", "asm_name", "submitter", "gbrs_paired_asm", "paired_asm_comp", "ftp_path", "excluded_from_refseq", "relation_to_type_material"))

chasemc

library(ggplot2)

execution_trace <- '/home/chase/Documents/pipeline_info/execution_trace_2021-08-14_09-52-45.txt' 

execution_trace <- read.delim(execution_trace, sep = "\t")
process_names <- sapply(strsplit(execution_trace$name, " "), function(x) x[[1]])


split_names <- strsplit(process_names, ":")
max_len <- max(lengths(split_names))

chasemc

library(data.table)
library(ggplot2)
library(gganimate)

population <- fread("/Users/chase/Downloads/csvData.csv") # https://worldpopulationreview.com/states
population <- population[, c("State", "Pop")]
colnames(population) <- c("state", "population")

covid <- "https://raw.githubusercontent.com/nytimes/covid-19-data/master/rolling-averages/us-states.csv"
covid <- fread(covid)

chasemc

parse_domtblout_file <- function(dom){
  dom = readLines(dom)
  dom <- dom[!grepl("^#", dom)]
  dom <- lapply(strsplit(dom, "[ ]{1,}"), 
                function(x){
                  parsed <- c(x[1:22], paste0(x[23:length(x)], collapse = " "))
                  as.data.frame(t(parsed))
                })
  dom <- do.call(rbind, dom)
  colnames(dom) <- c("target_name",

chasemc

[Main]
seed=632741178
phase=0
max_processors=24
dataset_id=RL
output_directory=out
temp_directory=/tmp
gsa=True
pooled_gsa=True

chasemc

library(data.table)
library(ggplot2)
library(lubridate)

df <- fread("Shootings.csv")

df$hour = lubridate::hour(lubridate::mdy_hms(df$Date))

new_df <- df[, list(arrest = sum(Arrest), no_arrest = sum(!Arrest), total_reports = length(Arrest)), Year]

chasemc

# Code is very loosely based on https://www.r-bloggers.com/r-cade-games-simulating-the-legendary-game-of-pong/

library(shiny)
library(ggvis)
library(dplyr)

# Playing field boundary lines
boundaries <- tibble(x = c(0, 50, 50, 0), y = c(0, 0, 50, 50))
paddleHeight <- tibble(x = c(0, 0), y = c(10, 20))

chasemc

---
title: "Display code language in Rmarkdown"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(eval = TRUE, include = TRUE, python.reticulate=FALSE)
```

```{r results="asis", echo=FALSE}

chasemc

for i in *.pdf; do
    inkscape --export-background-opacity=0 --export-dpi=300 --export-type=png $i
done

chasemc

## Emacs, make this -*- mode: sh; -*-

FROM r-base:latest

LABEL org.label-schema.license="GPL-2.0" \
      org.label-schema.vcs-url="https://github.com/rocker-org/rocker" \
      maintainer="Dirk Eddelbuettel <[email protected]>"

RUN apt-get update \
	&& apt-get install -y --no-install-recommends \