UQRUG 32

meeting
quanteda
ggplot2
msstats
meta
Overview: quanteda.
Questions: ggplot2 facets, MSstats, forest plot with meta
Published

October 26, 2022

2022-10-26: UQRUG 32

Attendees

  • Nick: Library | here to help
  • Luke: Library | here to help
  • Valentina: Library | here to help
  • Pierre: P&F | Listen and learn
  • Sophie:
  • Robyn:
  • Semira:
  • David: UQ-RCC | hopefully helpful ;-)
  • Christina: Psychology | Learn text analysis for R
  • Danelle:
  • Jaye:
  • Rene: Pharmacy | listen and learn
  • Rovan:
  • Roman:
  • Semira:
  • Sogra:
  • Kar:

Topics discussed and code

Presentation on quanteda

Nick Wiggins did a presentation on the quanteda package to give an overview and introduction to the package and how he has recently used it to assist a researcher. https://quanteda.io/

Kar ggplot facet_wrap label issue

Kar has the below sample data set:

MyID    eventA review   eventB review   eventC review
id_68   very good   neutral 
id_30   very good   very good   
id_15   good    very good   
id_1    neutral very good   
![](https://s3.hedgedoc.org/demo/uploads/6f9d7f0d-202b-4549-b7b1-186dbe9bb093.png)

He is trying to create a facet_wrap in ggplot that includes labels that are missing from the data, but needed to scale “bad” & “very bad”, while having the y labels showing on every facet. Without manually creating each y scale.

# Data transformation
trial %>% 
  pivot_longer(c(2:3), names_to = "events", values_to = "review") %>% 
  count(events, review) %>% 
  rbind(tibble(events = c("eventA review", "eventA review"),
               review = c("bad", "very bad"),
               n = c(NA, NA))) %>%
  mutate(events = as.factor(events),
         review = as.factor(review)) %>% 
# plot
  ggplot(aes(y = review, x = n, fill = events)) +
  geom_col(width = 0.5) +
  facet_wrap(~events) +
  theme(legend.position = "none")
Sogra stat comparison issue

Sogra has a large dataset of protein observations and needs to compare between different groups.

Using the package MSstats Sogra needs to re-export that data.

Semira

Semira is trying to change the colours of the diamonds in a forest plot created using the meta package. We’ve tried change the col.diamonds to set the colours, however this changed all of the boxes in the forest plot.