Chase Clark chasemc
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| utils::writeClipboard( | |
| paste0( | |
| "c(\n", | |
| paste0( | |
| sQuote(colnames(z), | |
| q = "ASCII"), | |
| sep = ",", | |
| collapse = "\n"), |
chasemc
/ hash_files.R
Last active
January 11, 2020 18:27
Generate a list of sha1 hashes given file paths
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| # requires openssl package | |
| hash_files <- function(paths){ | |
| num_paths <- length(paths) | |
| pb <- txtProgressBar(max=num_paths) | |
| lapply(seq_along(paths), function(x){ | |
| setTxtProgressBar(pb, x) | |
| flush.console() | |
| openssl::sha1(file(paths[[x]])) | |
| }) |
chasemc
/ idbac_programming_outline.rmd
Created
January 31, 2020 15:38
Outline of new IDBac functions for programming with IDBac
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| --- | |
| title: "Programming IDBac" | |
| author: "Chase Clark" | |
| date: "1/31/2020" | |
| output: html_document | |
| --- | |
| ```{r setup, include=FALSE} | |
| knitr::opts_chunk$set(eval = FALSE, include = TRUE) | |
| ``` |
chasemc
/ db_path_from_pool.R
Last active
March 15, 2020 17:02
Two functions: Check if an object is pool; Get path of database from pool
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| #' Check if a pool object | |
| #' | |
| #' @param pool variable to check | |
| .checkPool <- function(pool){ | |
| val <- all(inherits(pool, "Pool"), | |
| inherits(pool, "R6")) | |
| if (isFALSE(val)) { |
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| library(ggplot2) | |
| library(data.table) | |
| library(geofacet) | |
| library(grid) | |
| library(gganimate) | |
| # Accessed 2020-03-24 at 9pm CST | |
| confirmed <- data.table::fread("http://covidtracking.com/api/states/daily.csv") | |
| confirmed$date <- as.Date(as.character(confirmed$date), "%Y%m%d") | |
| confirmed <- confirmed[confirmed$date != "2020-03-24", ] |
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| N=5 | |
| for( i in 1:(N-1) ){ | |
| for( j in (i+1):N ){ | |
| print(paste(i,j)) | |
| } | |
| } |
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| protein | average | |
|---|---|---|
| RL29 [M+2H]2+ | 3637.8 | |
| RS32 [M+H]+ | 5096.8 | |
| RS34 [M+H]+ | 5381.4 | |
| RS33meth [M+H]+ | 6255.4 | |
| RL29 [M+H]+ | 7274.5 | |
| RS19 [M+H]+ | 10300.1 | |
| RNAse A [M+H]+ | 13683.2 | |
| Myoglobin [M+H]+ | 16952.3 |
chasemc
/ lca_height.R
Last active
May 7, 2020 22:40
Find the height of the least common ancestor of two nodes in a dendrogram in R (requires dendextend package)
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| # install.packages("dendexted") | |
| lca_height <- function(dend, | |
| input_a, | |
| input_b) { | |
| subtrees <- dendextend::partition_leaves(dend) | |
| find_ancestors <- function(input_labels) { | |
| which(sapply(subtrees, function(x) input_labels %in% x)) |
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| library(data.table) | |
| library(reshape2) | |
| library(ggplot2) | |
| a <- "https://covidtracking.com/api/v1/states/IL/daily.csv" | |
| a <- data.table::fread(a) | |
| a$date <- as.Date(as.character(a$date), "%Y%m%d") |
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| library(ggplot2) | |
| library(data.table) | |
| library(geofacet) | |
| raw_data <- data.table::fread("http://covidtracking.com/api/states/daily.csv") | |
| raw_data$date <- as.Date(as.character(raw_data$date), "%Y%m%d") | |
| raw_data <- raw_data[date > "2020-03-15", ] |