William E Fondrie, January 18, 2018
This repository contains the code required to reproduce the analysis presented in Pathogen Identification Direct from Polymicrobial Specimens Using Membrane Glycolipids. The data required for this analysis (data.zip below) can be downloaded from here. We are currently in the process of working with the UMB Office of Technology Transfer to provide a download link. In the interim, please contact dgoodlett@rx.umaryland.edu and the data will be provided to you promptly.
WARNING: When attempting to reproduce this analysis, it should be noted that Rmd/simulateCompleSpectra.Rmd requires approximately 36 Gb of memory to execute. Additionally, the entire analysis time may take a number of hours depending on the hardware.
Order of analysis (see the Rmd subdirectory for details):
- modelTraining.Rmd
- simulateComplexSpectra.Rmd
- mixtureAnalysis.Rmd
- evaluateModels.Rmd
- baselineClassifiers.Rmd
- makeMiscFigures.Rmd
- illustrations.Rmd
- makeTables.Rmd
To reproduce this analysis, the project directory must be structured as follows:
|- README.Rmd
|- data
| `- data.zip
|- R
| |- createNewFeatureTbl.R
| |- ggplotTheme.R
| |- utilityFunctions.R
| |- prepareData.R
| |- extract.R
| `- preProcessSpec.R
`- Rmd
|- baselineClassifiers.Rmd
|- evaluateModels.Rmd
|- illustrations.Rmd
|- makeMiscFigures.Rmd
|- mixtureAnalysis.Rmd
|- modelTraining.Rmd
|- simulateComplexSpectra.Rmd
`- writeTables.Rmd
This analysis uses a number of R packages. To ensure that all of them are installed on your machine, you can execute the following:
install.packages(c("tidyverse",
"stringr",
"forcats",
"MALDIquant",
"MALDIquantForeign",
"caret",
"PRROC",
"xgboost",
"tictoc",
"devtools",
"openxlsx",
"e1071",
"knitr",
"rmarkdown"))With a correctly prepared directory, the entire analysis can be run with a single line of code. If it is your fist time running the analysis, you can unzip the data/data.zip into the data directory manually, or change unzipData to TRUE in the next section.
To run the analysis:
rmarkdown::render("path/to/README.Rmd", envir = new.env())When this rmarkdown file is rendered, the following code is executed:
tictoc::tic()
unzipData <- FALSE # change to "TRUE" to unzip "data.zip" in the data directory
if(unzipData) {
unzip("data/data.zip", overwrite = T, exdir = "../data")
}
library(rmarkdown)
# Make results, temp and mdOutput directories:
dir.create("temp")
dir.create("results")
dir.create("Rmd/mdOutput")
# Set global parameters for analysis
mzTol <- 1.5 # m/z tolerance for feature extraction in Da
saveRDS(mzTol, "temp/mzTol.rds")The runAnalysis() function takes a list of .Rmd files and knits them into GitHub compatible markdown files.
runAnalysis <- function(rmd) {
lapply(rmd,
render,
envir = new.env(),
output_dir = "Rmd/mdOutput")
}
files <- c("modelTraining", # Trains xgboost models
"simulateComplexSpectra", # simulates polymicrobial spectra
"mixtureAnalysis", # Imports spectra from experimental two-species
"baselineClassifiers", # Implements simple baseline classifiers
"evaluateModels", # Calculate performance metrics and makes figures
"makeMiscFigures", # Creates additional figures
"illustrations", # Creates additional figures for illustrations
"writeTables") # Creates supplementarly Tables
files <- paste0("Rmd/", files, ".Rmd")Now run the analysis:
runAnalysis(files)times <- tictoc::toc()
cat(c("Execution time:", round((times$toc - times$tic)/60, 0), "min\n\n"))
session_info()## 3490.38 sec elapsed
## Execution time: 58 min
##
## setting value
## version R version 3.4.0 (2017-04-21)
## system x86_64, mingw32
## ui RTerm
## language (EN)
## collate English_United States.1252
## tz America/New_York
## date 2018-01-18
##
## package * version date source
## assertthat 0.2.0 2017-04-11 CRAN (R 3.3.3)
## backports 1.1.0 2017-05-22 CRAN (R 3.4.0)
## base * 3.4.0 2017-04-21 local
## base64enc 0.1-3 2015-07-28 CRAN (R 3.2.1)
## broom * 0.4.2 2017-02-13 CRAN (R 3.4.0)
## car 2.1-4 2016-12-02 CRAN (R 3.4.0)
## caret * 6.0-76 2017-04-18 CRAN (R 3.4.0)
## cellranger 1.1.0 2016-07-27 CRAN (R 3.4.0)
## class 7.3-14 2015-08-30 CRAN (R 3.4.0)
## codetools 0.2-15 2016-10-05 CRAN (R 3.4.0)
## colorspace 1.3-2 2016-12-14 CRAN (R 3.4.0)
## compiler 3.4.0 2017-04-21 local
## data.table 1.10.4 2017-02-01 CRAN (R 3.4.0)
## datasets * 3.4.0 2017-04-21 local
## DBI 0.6-1 2017-04-01 CRAN (R 3.4.0)
## devtools * 1.13.2 2017-06-02 CRAN (R 3.4.0)
## digest 0.6.12 2017-01-27 CRAN (R 3.4.0)
## dplyr * 0.5.0 2016-06-24 CRAN (R 3.4.0)
## e1071 1.6-8 2017-02-02 CRAN (R 3.4.0)
## evaluate 0.10 2016-10-11 CRAN (R 3.4.0)
## forcats * 0.2.0 2017-01-23 CRAN (R 3.4.0)
## foreach 1.4.3 2015-10-13 CRAN (R 3.4.0)
## foreign 0.8-68 2017-04-24 CRAN (R 3.4.0)
## ggplot2 * 2.2.1 2016-12-30 CRAN (R 3.4.0)
## graphics * 3.4.0 2017-04-21 local
## grDevices * 3.4.0 2017-04-21 local
## grid 3.4.0 2017-04-21 local
## gtable 0.2.0 2016-02-26 CRAN (R 3.4.0)
## haven 1.0.0 2016-09-23 CRAN (R 3.4.0)
## hms 0.3 2016-11-22 CRAN (R 3.4.0)
## htmltools 0.3.6 2017-04-28 CRAN (R 3.4.0)
## httr 1.2.1 2016-07-03 CRAN (R 3.4.0)
## iterators 1.0.8 2015-10-13 CRAN (R 3.4.0)
## jsonlite 1.4 2017-04-08 CRAN (R 3.4.0)
## knitr 1.16 2017-05-18 CRAN (R 3.4.0)
## labeling 0.3 2014-08-23 CRAN (R 3.4.0)
## lattice * 0.20-35 2017-03-25 CRAN (R 3.4.0)
## lazyeval 0.2.0 2016-06-12 CRAN (R 3.4.0)
## lme4 1.1-13 2017-04-19 CRAN (R 3.4.0)
## lubridate 1.6.0 2016-09-13 CRAN (R 3.4.0)
## magrittr 1.5 2014-11-22 CRAN (R 3.4.0)
## MALDIquant * 1.16.2 2017-04-04 CRAN (R 3.4.0)
## MALDIquantForeign * 0.10 2015-11-01 CRAN (R 3.4.0)
## MASS 7.3-47 2017-02-26 CRAN (R 3.4.0)
## Matrix 1.2-10 2017-04-28 CRAN (R 3.4.0)
## MatrixModels 0.4-1 2015-08-22 CRAN (R 3.4.0)
## memoise 1.1.0 2017-04-21 CRAN (R 3.4.0)
## methods * 3.4.0 2017-04-21 local
## mgcv 1.8-17 2017-02-08 CRAN (R 3.4.0)
## minqa 1.2.4 2014-10-09 CRAN (R 3.4.0)
## mnormt 1.5-5 2016-10-15 CRAN (R 3.4.0)
## ModelMetrics 1.1.0 2016-08-26 CRAN (R 3.4.0)
## modelr 0.1.0 2016-08-31 CRAN (R 3.4.0)
## munsell 0.4.3 2016-02-13 CRAN (R 3.4.0)
## nlme 3.1-131 2017-02-06 CRAN (R 3.4.0)
## nloptr 1.0.4 2014-08-04 CRAN (R 3.4.0)
## nnet 7.3-12 2016-02-02 CRAN (R 3.4.0)
## openxlsx * 4.0.17 2017-03-23 CRAN (R 3.4.2)
## parallel 3.4.0 2017-04-21 local
## pbkrtest 0.4-7 2017-03-15 CRAN (R 3.4.0)
## plyr 1.8.4 2016-06-08 CRAN (R 3.4.0)
## PRROC * 1.3 2017-04-21 CRAN (R 3.4.0)
## psych 1.7.5 2017-05-03 CRAN (R 3.4.0)
## purrr * 0.2.2.2 2017-05-11 CRAN (R 3.4.0)
## quantreg 5.33 2017-04-18 CRAN (R 3.4.0)
## R6 2.2.1 2017-05-10 CRAN (R 3.4.0)
## Rcpp 0.12.11 2017-05-22 CRAN (R 3.4.0)
## readBrukerFlexData 1.8.5 2017-04-22 CRAN (R 3.4.0)
## readMzXmlData 2.8.1 2015-09-16 CRAN (R 3.4.0)
## readr * 1.1.1 2017-05-16 CRAN (R 3.4.0)
## readxl 1.0.0 2017-04-18 CRAN (R 3.4.0)
## reshape2 1.4.2 2016-10-22 CRAN (R 3.4.0)
## rlang 0.1.1 2017-05-18 CRAN (R 3.4.0)
## rmarkdown * 1.6 2017-06-15 CRAN (R 3.4.2)
## rprojroot 1.2 2017-01-16 CRAN (R 3.4.0)
## rstudioapi 0.6 2016-06-27 CRAN (R 3.4.0)
## rvest 0.3.2 2016-06-17 CRAN (R 3.4.0)
## scales 0.4.1 2016-11-09 CRAN (R 3.4.0)
## SparseM 1.77 2017-04-23 CRAN (R 3.4.0)
## splines 3.4.0 2017-04-21 local
## stats * 3.4.0 2017-04-21 local
## stats4 3.4.0 2017-04-21 local
## stringi 1.1.5 2017-04-07 CRAN (R 3.4.0)
## stringr * 1.2.0 2017-02-18 CRAN (R 3.4.0)
## tibble * 1.3.1 2017-05-17 CRAN (R 3.4.0)
## tictoc 1.0 2014-06-17 CRAN (R 3.4.0)
## tidyr * 0.6.3 2017-05-15 CRAN (R 3.4.0)
## tidyverse * 1.1.1 2017-01-27 CRAN (R 3.4.0)
## tools 3.4.0 2017-04-21 local
## utils * 3.4.0 2017-04-21 local
## withr 1.0.2 2016-06-20 CRAN (R 3.4.0)
## xgboost * 0.6-4 2017-01-05 CRAN (R 3.4.1)
## XML 3.98-1.7 2017-05-03 CRAN (R 3.4.0)
## xml2 1.1.1 2017-01-24 CRAN (R 3.4.0)
## yaml 2.1.14 2016-11-12 CRAN (R 3.4.0)