all analyses re-knitted

analysis/FITS1/FITS1_Analysis_pipeline_v4-3.Rmd

 ---
-title: "16S Data Analysis"
+title: "FITS1 Data Analysis"
 author: "Simeon Lim Rossmann, Marte Persdatter Tangvik"
 date: "23.12.2024"
 output:
@@ -86,7 +86,7 @@ remotes::install_github("mahendra-mariadassou/phyloseq-extended", ref = "dev")
 source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R" )
 
 library(phyloseq)
-library(SIAMCAT)
+#library(SIAMCAT)
 
 # Phylogeny libraries
 library(phangorn)
@@ -676,7 +676,7 @@ its1_percentage
 
 This chunk plots abundance of the Top n ASVs or taxa at a given level as a bar plot, giving an insight into the presence of the n ASV and most common taxa for the primary and secondary parameters. The default for n is set at 20, a larger n may lead to delay/skipping of the plot in standard out, but it should be saved as a PDF regardless for ASVs. For taxa, a large n  may lead to unreadable plots. **The chunk does not require any input**, but it is possible to adjust the **default 'n'**, and to change **width**, **height** and **resolution** of the PDF-output if necessary.
 
-```{r custom-Bar-plot, tidy=TRUE, message=FALSE}
+```{r custom Bar plot, message=FALSE}
 # CHANGE ME to the desired sample categories on the x-axis. 
 # Accepted values are the column headers in the descriptor file.
 set$x_axis_value = "ndvi"
@@ -785,7 +785,7 @@ plots$combo_topn_custom
 
 ### NDVI+Shannon regression
 
-```{r ndvi-shannon}
+```{r ndvi shannon}
 topntax_data <- set$topntax_tbl %>%
   mutate(Taxa = 'fits1') %>%
   ungroup() %>%
@@ -799,7 +799,7 @@ write.csv(topntax_data, file = "../topntax_all_taxa/topntax_data_fits1.csv")
 ### NDVI regression 
 
 
-```{r NDVI-new}
+```{r NDVI new}
 
 # Create properly formatted tibble with columns Sample, ndvi_01 (ndvi translated to (0, 1) interval) and one column for each genus
 # containing the sample abundances for that genus.

analysis/FITS2/FITS2_Analysis_pipeline_v4-3.Rmd

 ---
-title: "16S Data Analysis"
+title: "FITS2 Data Analysis"
 author: "Simeon Lim Rossmann, Marte Persdatter Tangvik"
 date: "23.12.2024"
 output:
@@ -86,7 +86,7 @@ remotes::install_github("mahendra-mariadassou/phyloseq-extended", ref = "dev")
 source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R" )
 
 library(phyloseq)
-library(SIAMCAT)
+#library(SIAMCAT)
 
 # Phylogeny libraries
 library(phangorn)
@@ -668,7 +668,7 @@ its2_percentage
 
 This chunk plots abundance of the Top n ASVs or taxa at a given level as a bar plot, giving an insight into the presence of the n ASV and most common taxa for the primary and secondary parameters. The default for n is set at 20, a larger n may lead to delay/skipping of the plot in standard out, but it should be saved as a PDF regardless for ASVs. For taxa, a large n  may lead to unreadable plots. **The chunk does not require any input**, but it is possible to adjust the **default 'n'**, and to change **width**, **height** and **resolution** of the PDF-output if necessary.
 
-```{r custom-Bar-plot, tidy=TRUE, message=FALSE}
+```{r custom-Bar-plot, message=FALSE}
 
 # CHANGE ME to the desired sample categories on the x-axis. 
 # Accepted values are the column headers in the descriptor file.
@@ -786,7 +786,7 @@ topntax_data <- set$topntax_tbl %>%
   select(Alias, ndvi, Shannon, Taxa) %>%
   distinct()
 
-write.csv(topntax_data, file = "../../topntax_all_taxa/topntax_data_fits2.csv")
+write.csv(topntax_data, file = "../topntax_all_taxa/topntax_data_fits2.csv")
 
 
 ```

analysis/Nems/Nems_Analysis_pipeline_v4-3.Rmd

 ---
-title: "16S Data Analysis"
+title: "Nems Data Analysis"
 author: "Simeon Lim Rossmann, Marte Persdatter Tangvik"
 date: "23.12.2024"
 output:
@@ -88,7 +88,7 @@ remotes::install_github("mahendra-mariadassou/phyloseq-extended", ref = "dev")
 source("https://raw.githubusercontent.com/mahendra-mariadassou/phyloseq-extended/master/load-extra-functions.R" )
 
 library(phyloseq)
-library(SIAMCAT)
+#library(SIAMCAT)
 
 # Phylogeny libraries
 library(phangorn)
@@ -811,7 +811,7 @@ plots$topn_ASVs
 
 This chunk plots abundance of the Top n ASVs or taxa at a given level as a bar plot, giving an insight into the presence of the n ASV and most common taxa for the primary and secondary parameters. The default for n is set at 20, a larger n may lead to delay/skipping of the plot in standard out, but it should be saved as a PDF regardless for ASVs. For taxa, a large n  may lead to unreadable plots. **The chunk does not require any input**, but it is possible to adjust the **default 'n'**, and to change **width**, **height** and **resolution** of the PDF-output if necessary.
 
-```{r custom-Bar-plot, tidy=TRUE, message=FALSE}
+```{r custom-Bar-plot, message=FALSE}
 # CHANGE ME to the desired sample categories on the x-axis. 
 # Accepted values are the column headers in the descriptor file.
 set$x_axis_value = "ndvi"
@@ -939,7 +939,7 @@ topntax_data <- set$topntax_tbl %>%
   select(Alias, ndvi, Shannon, Taxa) %>%
   distinct()
 
-write.csv(topntax_data, file = "../../topntax_all_taxa/topntax_data_nematodes.csv")
+write.csv(topntax_data, file = "../topntax_all_taxa/topntax_data_nematodes.csv")
 
 
 ```
@@ -1261,13 +1261,13 @@ set$data_mol_morph_long <- data_mol_morph_long_temp %>%
 
 set$data_morph <- set$data_mol_morph_long[set$data_mol_morph_long$type == 'total_count',]
 set$data_morph <- set$data_morph %>%
-  rename("value" = "Number_of_nematodes")
+  dplyr::rename("Number_of_nematodes" = value)
 
 # Relative abundance data
 
 set$data_relabu <- set$data_mol_morph_long[set$data_mol_morph_long$type == 'Genus_Sample_Abundance',]
 set$data_relabu <- set$data_relabu %>%
-  rename("value" = "Relative_abundance")
+  dplyr::rename("Relative_abundance" = value)
 ```