Merge pull request #24 from AleruDivine/main

Updated vignettes

Author: cmirzayi

bugSigSimple.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: b8714a68-b332-4c39-88f2-49fdba065555
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

vignettes/c-section_meconium_shaimaa.Rmd

@@ -86,8 +86,14 @@ subset.final <-
   arrange(PMID)
 ```
 Show key characteristics of the included signatures:
+
+```{r}
+detach("package:dplyr", unload = TRUE)
+library(dplyr)
+```
+
 ```{r}
-select(subset.final, all_of(c("PMID", "Source", "Group 0 name", "Group 1 name", "Abundance in Group 1")))
+select(subset.final, "PMID", "Source", "Group 0 name", "Group 1 name", "Abundance in Group 1")
 ```
 
 Are any studies missing?

vignettes/capstoneanalysis_clare.rmd

@@ -44,17 +44,22 @@ covid_all <- bugsigdbr::subsetByOntology(dat, column = "Condition", "COVID-19",
   mutate(studyexp = paste(Study, Experiment, sep = "_")) %>%
   mutate(
     site = recode(`Body site`,
-      "feces" = "Gut",
-      "rectal" = "Gut",
-      "nasopharynx" = "aURT",
-      "oropharynx" = "aURT",
-      "nasopharynx,oropharynx" = "aURT",
-      "tongue" = "aURT"
+      "Feces" = "Gut",
+      "Rectum" = "Gut",
+      "Nasopharynx" = "aURT",
+      "Oropharynx" = "aURT",
+      "Nasopharynx,Oropharynx" = "aURT",
+      "Nasal cavity" = "aURT",
+      "Surface of tongue" = "aURT",
+      "Nasopharynx,Throat" = "aURT",
+      "Throat" = "aURT",
+      "Tongue" = "aURT",
+      "Lung" = "LRT",
+      "Sputum" = "LRT"
     )
   ) %>%
   mutate(comparison1 = paste(`Group 0 name`, `Group 1 name`, sep = " vs "))
 ```  
-  
 
 ## Table of studies
 
@@ -73,6 +78,10 @@ gut_sigs <- filter(covid_all,
 
 naso_sigs <- filter(covid_all, 
                            site == "aURT") %>%
+    drop_na(Source)
+  
+resp_sigs <- filter(covid_all, 
+                           site == "LRT") %>%
   drop_na(Source)
 ```
 
@@ -88,6 +97,10 @@ kableExtra::kbl(bugSigSimple::createTaxonTable(gut_sigs))
 kableExtra::kbl(bugSigSimple::createTaxonTable(naso_sigs))
 ```
 
+```{r}
+kableExtra::kbl(bugSigSimple::createTaxonTable(resp_sigs))
+```
+
 # gut microbiota analysis
 
 Look specifically at case-control comparisons

vignettes/capstoneanalysis_fatima.rmd

@@ -39,12 +39,12 @@ dim(dat)
 ```{r}
 my.dat <- subsetByCurator(dat, curator="Fatima Zohra")
 table(my.dat[,"Condition"])
-condsnew <-c("bipolar disorder","unipolar depression")
+condsnew <-c("bipolar disorder","major depressive disorder")
 condsnew <-c("bipolar disorder")
 
 efo <- bugsigdbr::getOntology("efo")
 dat.bpd <- bugsigdbr::subsetByOntology(dat, column = "Condition", "bipolar disorder", efo)
-dat.upd <- bugsigdbr::subsetByOntology(dat, column = "Condition", "unipolar depression", efo)
+dat.upd <- bugsigdbr::subsetByOntology(dat, column = "Condition", "major depressive disorder", efo)
 my.dat.cond <- rbind(dat.bpd, dat.upd)
 table(my.dat.cond[,"Condition"])
 
@@ -104,9 +104,9 @@ my.dat.mdd <- my.dat.cond[!ind,]
 dim(my.dat.mdd)
 table(my.dat.mdd[,"Condition"])
 
-getMostFrequentTaxa(my.dat.mdd, n=20)
-getMostFrequentTaxa(my.dat.mdd,sig.type= "increased")
-getMostFrequentTaxa(my.dat.mdd,sig.type= "decreased")
+getMostFrequentTaxa(my.dat.mdd, n= 20)
+getMostFrequentTaxa(my.dat.mdd,, "UP")
+getMostFrequentTaxa(my.dat.mdd,, "DOWN")
 ```
 
 ## Binomial test "Increased in bipolar"

vignettes/capstoneanalysis_kweku.rmd

@@ -57,7 +57,7 @@ bugSigSimple::createStudyTable(dat_condition)
 
 ```{r}
 gut_sigs <- filter(dat_condition,
-                   `Body site` %in% c("feces,mucosa of small intestine", "feces"))
+                   `Body site` %in% c("Feces, Mucosa of small intestine", "Feces"))
 ```
 
 In this table, the Binomial Test p-value corresponds to the null hypothesis

vignettes/fieldworkanalysis_samara.Rmd

@@ -221,11 +221,12 @@ fit.negbin <-
     data = df,
     control = glm.control(
       epsilon = 1e-8,
-      maxit = 70,
+      maxit = 50,
       trace = FALSE
     )
   )
-summary(fit.negbin)
+library(broom)
+tidy(fit.negbin)
 
 fit.ZInegbin <- zeroinfl(Streptococcus ~ Lactobacillus + age + BMI | 1,
                 data = df,

vignettes/healthysig.Rmd

@@ -175,8 +175,8 @@ overlap0_increased<- merge(x = bugall_increased, y = paircheck0_increased, by =c
 overlap0_increased[is.na(overlap0_increased)] <- 0  
 ```
 
-
 #```{r comparison-increased_vs_decrease}
+```
 t.test(overlap0_increased$overlap, overlap0_decreased$overlap)
 wilcox.test(overlap0_increased$overlap, overlap0_decreased$overlap)