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Refactor Shaimaa's meconium vignette for efficiency and correctness #42

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Merged
lwaldron merged 2 commits into from
Jun 1, 2026
Merged

Refactor Shaimaa's meconium vignette for efficiency and correctness #42

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7b5a3e9
Refactor Shaimaa's meconium vignette for efficiency and correctness
lwaldron Jun 1, 2026
dc68a13
Add acknowledgement to Gemini Code Assist
lwaldron Jun 1, 2026
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35 changes: 19 additions & 16 deletions vignettes/c-section_meconium_shaimaa.Rmd
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ vignette: >
# Making sure packages are installed

Not evaluated in vignette:
```{r, eval=FALSE, messages=FALSE}
```{r, eval=FALSE, message=FALSE}
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("devtools", "tidyverse", "kableExtra"))
Expand All @@ -28,15 +28,13 @@ BiocManager::install(c("waldronlab/bugSigSimple", "waldronlab/BugSigDBStats", "w

# Load and subset data

```{r, messages=FALSE}
```{r, message=FALSE}
suppressPackageStartupMessages({
library(bugSigSimple)
library(BugSigDBStats)
library(bugsigdbr)
library(tidyverse)
library(stringr)
library(kableExtra)
library(dplyr)
})
```

Expand All @@ -49,7 +47,7 @@ names(dat)

# Subsetting

```{r, messages=FALSE}
```{r, message=FALSE}
included.pmid <-
c(
28018325,
Expand All @@ -64,7 +62,8 @@ included.pmid <-
27362264
)
subset.dat <-
filter(dat, PMID %in% included.pmid)
dat %>%
dplyr::filter(PMID %in% included.pmid)
```

```{r group0}
Expand All @@ -81,20 +80,17 @@ included.group1 <- "C-section"

```{r}
subset.final <-
filter(subset.dat, `Group 0 name` %in% included.group0 & `Group 1 name` %in% included.group1) %>%
filter(`Body site` == "Meconium") %>%
arrange(PMID)
subset.dat %>%
dplyr::filter(`Group 0 name` %in% included.group0, `Group 1 name` %in% included.group1) %>%
dplyr::filter(`Body site` == "Meconium") %>%
dplyr::arrange(PMID)
```

Show key characteristics of the included signatures:

```{r}
detach("package:dplyr", unload = TRUE)
library(dplyr)
```

```{r}
select(subset.final, "PMID", "Source", "Group 0 name", "Group 1 name", "Abundance in Group 1")
subset.final %>%
dplyr::select("PMID", "Source", "Group 0 name", "Group 1 name", "Abundance in Group 1")
```

Are any studies missing?
Expand All @@ -120,7 +116,9 @@ createStudyTable(subset.final) %>%
This table summarizes the results for the top `n` most frequently identified taxa.

```{r}
kable_styling(kbl(bugSigSimple::createTaxonTable(subset.final, n = 20)))
bugSigSimple::createTaxonTable(subset.final, n = 20) %>%
kbl() %>%
kable_styling()
```


Expand All @@ -139,3 +137,8 @@ getMostFrequentTaxa(subset.final, direction="UP")
```{r}
getMostFrequentTaxa(subset.final, direction="DOWN")
```

# Acknowledgements

This vignette was refactored with the assistance of Gemini Code Assist.

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