cleans up PTM masterlist and aggregates photos, sequences and freezer contents
- get access to Martone Lab server via Botany IT (photos or sequences) -> or use Martone Lab Computer
- get access to PTM Master List
- have R and IDE (ie. Rstudio) installed
run these lines of code in your Console if you use RStudio
install.packages("tidyverse","leaflet","readxl","janitor","googlesheets4")
devtools::install_github("martonelab/ptm")
- 2020 March Note
googlesheets4
-write_sheets
functionality is not on CRAN yet:devtools::install_github("tidyverse/googlesheets4")
01_metadata_cleaning
- standarizes text data and coordinate data02_integrate_photos
- checks the photos on the Martone Lab server and adds the information to the masterlist03_integrate_sequences
- checks the sequences on the Martone Lab server and adds the corresponding information04_integrate_freezer
- updates the Master List based upon the freezer inventory done in January 2020
- Note all the code templates saves the files to the
output folder
and can be run independently
- server:
martonelab/Lab Operation/masterlist_archive
- save as: YYYYMMMDD_PTM - Master List.xlsx
- ie.
2020Mar18_PTM - Master List.xlsx
- Clean from top to bottom
- run code files 01 to 04 in sequence
- Update photos or sequences
- run the corresponding code file (02 or 03)
- default is to save to the masterlist
- review columns after the code is run
- keep the columns after
Following these rules will ensure all information gets reflected properly when combined.
- PTM[insert number here].jpg
- no spaces!
- ie. PTM1234.jpg
- please follow Nanuq guidelines
- PTM[Number] __ [primername] __ [additional info provided by nanuq]
- ie. PTM1500_TLF5_P1512217_076.ab1 (underscores)
- should not be in any additional folders
- Currently accepted primers: "rbclrevnew", "gwsfn", "gwsrx", "psbar2", "psbaf", "F7553", "f|F57", "R1150K"