UQRUG 7

meeting
tmap
stylr
raster
ggplot2
ggpubr
thermimage
ggir
mertools
xml
sas
Questions: quosure and quasiquotation, favourite packages, reading XML data, SAS to R migration, RNAseq
Published

July 27, 2020

2020-07-27: UQRUG 7

On Zoom, 3-5 pm.

Attendees and problems

  • Stéphane (Library): anyone with experience with Tidyverse + quosure / quasiquotation? I want to use strings in one column as object names in a function.
  • Ruth (HMNS): I don’t have any specific issues this week. I am happy to listen and explore new packages.
  • Chantelle Derez (Biological Science): I don’t have any specific issues, just popping in to learn. Current favourite package is Thermimage and colour palette ‘rainbow’ for analysing thermal images. :rainbow:
  • Paula Andrea M (CAI) I’m here to help. Also I would like to invite you to the Rladies Brisbane events. https://www.meetup.com/rladies-brisbane/events/272075776 The topic of next month is R in Biology.
  • Fathin (SAFS) No issue to date.
  • Damber (I want to learn plotting glmm prediction) - shared on chat.uq.edu as well.
  • Candice: RNAseq in R.
    • Found resources:
    • https://osca.bioconductor.org
    • https://bioconductor.riken.jp/packages/3.8/workflows/html/simpleSingleCell.html
  • Greg (Chemical Engineering) Late but here to help. Currently grappling with some nasty XML at the moment that I want to parse efficiently. Writing my PhD thesis in RMarkdown.

Favourite packages

  • tmap: https://mtennekes.github.io/tmap/
  • stylr: https://github.com/r-lib/styler
  • raster: https://rspatial.org/raster/pkg/index.html
  • ggplot2: https://ggplot2.tidyverse.org/
    • ggpubr: https://rpkgs.datanovia.com/ggpubr/index.html
  • Thermimage: https://cran.r-project.org/web/packages/Thermimage/index.html
  • GGIR: https://cran.r-project.org/web/packages/GGIR/index.html

From today’s questions

  • Reading XML data into R
    • https://subscription.packtpub.com/book/big_data_and_business_intelligence/9781783989065/1/ch01lvl1sec11/reading-xml-data
    • https://stackoverflow.com/questions/40977885/extracting-nodes-by-name
    • Greg also this code worked well for missing nodes, but not for repeated names. Have a try
library(XML)
library(methods)

xmldata <- xmlToDataFrame("data/plant_catalog_incomplete.xml")
View(xmldata)
  • For Single cell analysis
    • https://osca.bioconductor.org/introduction.html
    • https://bioconductor.riken.jp/packages/3.8/workflows/html/simpleSingleCell.html
  • For plotting gml data
    • merTools https://rdrr.io/cran/merTools/man/plotREsim.html
    • https://easystats.github.io/see/articles/performance.html
  • SAS to R migration
    • https://www.r-bloggers.com/sas-to-r-migration/
    • https://github.com/asnr/sas-to-r