This is an archive for the R codes used in the data analysis pipeline to export and analyze the strawberry imaging mass spectrometry data in the reference publication listed below.
Data was acquired with the Bruker MALDI ultraflextreme using flexControl 3.4 and flexImaging 4.0 and in the condensed .d format.
- script.R contains the entire script used for the data analysis
- functions.R contains the functions written by Ethan Yang and called during the script
Jin Wang, Ethan Yang, Pierre Chaurand, Vijaya Raghavan. Visualizing the distribution of strawberry plant metabolites at different maturity stages by MALDI-TOF imaging mass spectrometry. Food Chem. 2020 Dec 10;345:128838. Online ahead of print. doi:10.1016/j.foodchem.2020.128838
- Ethan Yang: Wrote 100% of the R codes for exporting and analyzing the IMS data currently available in this repository
- Jin Wang: Exported the IMS results for visualization, provided the statistical analysis for all data (HPLC and IMS)
- Pierre Chaurand: Provided guidance and outlined the data analysis pipeline; corrected figures
- Vijaya Raghavan: Verified final data analysis
- Cardinal for reading MALDI imaging data
- MALDIquant and MALDIquantForeign for obtaining peak intensities and peak picking
- Tidyverse for data wrangling and summarizing after peak picking
This repository contains only the scripts and functions for analyzing the imaging mass spectrometry data, not the HPLC-UV data also included in the publication. The session info provided below were determined post publication and therefore may not be an accurate representation of the actual R enviornment during data analysis. The scripts provided have been scrapped to remove any personal identifying information.
Please reference the LICENSE document for details.
RStudio: Version 1.3.959
R version: 3.4.4
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Attached base packages:
- parallel
- stats
- graphics
- grDevices utils
- datasets
- methods
- base
Other attached packages:
- MALDIquant_1.17
- XML_3.98-1.10
- Cardinal_1.2.1
- ProtGenerics_1.10.0
- Biobase_2.38.0
- BiocGenerics_0.24.0
loaded via a namespace (and not attached):
- Rcpp_0.12.16
- MASS_7.3-49
- lattice_0.20-35
- R6_2.2.2
- rlang_0.2.0
- tools_3.4.4
- grid_3.4.4
- irlba_2.3.2
- yaml_2.1.19
- mmand_1.5.3
- Matrix_1.2-12
- signal_0.7-6
- sp_1.2-7
- compiler_3.4.4
- stats4_3.4.4
R version: 3.6.0
R version 3.6.0 (2019-04-26)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
attached base packages:
- stats4
- parallel
- stats
- graphics
- grDevices utils
- datasets
- methods
- base
other attached packages:
- forcats_0.5.0
- stringr_1.4.0
- dplyr_0.8.5
- purrr_0.3.4
- readr_1.3.1
- tidyr_0.8.3
- tibble_3.0.1
- ggplot2_3.3.0
- tidyverse_1.2.1
- MALDIquant_1.19.3
- Biobase_2.44.0
- XML_3.99-0.3
- Cardinal_2.2.5
- ProtGenerics_1.16.0
- S4Vectors_0.22.1
- EBImage_4.26.0
- BiocParallel_1.18.1
- BiocGenerics_0.30.0
loaded via a namespace (and not attached):
- httr_1.4.1
- jsonlite_1.6.1
- viridisLite_0.3.0
- modelr_0.1.4
- assertthat_0.2.1
- sp_1.3-1
- tiff_0.1-5
- cellranger_1.1.0
- yaml_2.2.0
- pillar_1.4.4
- backports_1.1.6
- lattice_0.20-38
- glue_1.4.0
- digest_0.6.25
- rvest_0.3.4
- colorspace_1.4-1
- MALDIquantForeign_0.12
- htmltools_0.4.0
- Matrix_1.2-17
- pkgconfig_2.0.3
- broom_0.5.6
- biglm_0.9-1
- haven_2.2.0
- fftwtools_0.9-8
- scales_1.1.0
- jpeg_0.1-8.1
- generics_0.0.2
- ellipsis_0.3.0
- withr_2.2.0
- cli_2.0.2
- magrittr_1.5
- crayon_1.3.4
- readxl_1.3.1
- mclust_5.4.3
- fansi_0.4.1
- nlme_3.1-139
- MASS_7.3-51.4
- xml2_1.2.0
- tools_3.6.0
- hms_0.5.3
- lifecycle_0.2.0
- munsell_0.5.0
- locfit_1.5-9.1
- irlba_2.3.3
- compiler_3.6.0
- signal_0.7-6
- rlang_0.4.6
- grid_3.6.0
- RCurl_1.95-4.12
- rstudioapi_0.11
- htmlwidgets_1.5.1
- bitops_1.0-6
- base64enc_0.1-3
- gtable_0.3.0
- abind_1.4-5
- DBI_1.1.0
- mmand_1.6.1
- R6_2.4.1
- lubridate_1.7.4
- stringi_1.4.3
- matter_1.10.0
- readMzXmlData_2.8.1
- Rcpp_1.0.4.6
- vctrs_0.2.4
- readBrukerFlexData_1.8.5
- png_0.1-7
- tidyselect_0.2.5