From dbb8dddd507561f6484d05a5da8de6c225dfede8 Mon Sep 17 00:00:00 2001
From: sdgamboa <samuel.gamboa.tuz@gmail.com>
Date: Mon, 11 Mar 2024 17:02:03 -0400
Subject: [PATCH] Update vignette with code for getting taxid from scientific
 name using taxize.

---
 vignettes/bugphyzz.Rmd | 13 +++++++++++--
 1 file changed, 11 insertions(+), 2 deletions(-)

diff --git a/vignettes/bugphyzz.Rmd b/vignettes/bugphyzz.Rmd
index f342a5dd..1e60445a 100644
--- a/vignettes/bugphyzz.Rmd
+++ b/vignettes/bugphyzz.Rmd
@@ -270,10 +270,19 @@ knitr::kable(gsea_tbl)
 Finally, a user could get all of the signature names to which a given taxon
 belongs to. Only taxids should be used.
 
-An example using _Escherichia coli_ (taxid: 562):
+An example using _Escherichia coli_ (taxid: 562).
+
+Get taxid for _E. coli_ using taxize:
+
+```{r, message=FALSE}
+taxid <- as.character(taxize::get_uid("Escherichia coli"))
+taxid
+```
+
+Get all signature names related to the _E. coli_ taxid:
 
 ```{r}
-getTaxonSignatures(tax = "562", bp = bp)
+getTaxonSignatures(tax = taxid, bp = bp)
 ```
 ## Session information: