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apallejaapalleja
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TRAINING_DIR to snake_case style
1 parent 977f763 commit 256e3f0

5 files changed

Lines changed: 30 additions & 25 deletions

‎tutorial/01_Alpha-diversity_tutorial.Rmd‎

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@@ -112,18 +112,22 @@ library(FSA)
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**Load species abundance, taxonomical annotation and metadata file**
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```{r, warning=FALSE}
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TRAINING_DIR <- "/workspaces/dsp_metagenomics_training/"
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training_dir <- "/workspaces/dsp_metagenomics_training/"
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```
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```{r, warning=FALSE}
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abundance <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAbundance_Species.rds"))
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abundance <- readRDS(file = paste0(training_dir,
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"data/MetaphlanAbundance_Species.rds"))
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rownames(abundance) <- gsub("_SRR_db1.metaphlan", "", rownames(abundance))
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# Taxonomical annotation
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annotation <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAnnotations_Species.rds"))
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annotation <- readRDS(file = paste0(training_dir,
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"data/MetaphlanAnnotations_Species.rds"))
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# Metadata
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metadata <- read.table(file = paste0(TRAINING_DIR, "data/metadata.tsv"), header = TRUE,
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metadata <- read.table(file = paste0(training_dir,
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"data/metadata.tsv"),
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header = TRUE,
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sep = "\t",
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quote = "",
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row.names = NULL)
@@ -150,7 +154,7 @@ abundance <- abundance[rownames(metadata), ]
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## Creating a directory for the related results
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```{r, warning=FALSE}
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results_dir <- paste0(TRAINING_DIR, "results/report/01_Alpha-diversity/")
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results_dir <- paste0(training_dir, "results/report/01_Alpha-diversity/")
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dir.create(results_dir,
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recursive = TRUE,

‎tutorial/02_Beta-diversity_tutorial.Rmd‎

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@@ -117,19 +117,19 @@ library(vegan)
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**Load species abundance, taxonomical annotation and metadata file**
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```{r}
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TRAINING_DIR <- "/workspaces/dsp_metagenomics_training/"
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training_dir <- "/workspaces/dsp_metagenomics_training/"
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```
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```{r}
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# Abundance table
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abundance <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAbundance_Species.rds"))
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abundance <- readRDS(file = paste0(training_dir, "data/MetaphlanAbundance_Species.rds"))
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rownames(abundance) <- gsub("_SRR_db1.metaphlan", "", rownames(abundance))
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# Taxonomical annotation
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annotation <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAnnotations_Species.rds"))
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annotation <- readRDS(file = paste0(training_dir, "data/MetaphlanAnnotations_Species.rds"))
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# Metadata
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metadata <- read.table(file = paste0(TRAINING_DIR, "data/metadata.tsv"), header = TRUE,
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metadata <- read.table(file = paste0(training_dir, "data/metadata.tsv"), header = TRUE,
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sep = "\t",
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quote = "",
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row.names = NULL)
@@ -141,7 +141,7 @@ abundance <- abundance[rownames(metadata), ]
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# Creating a directory for the PCoA related results
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```{r}
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results_dir <- paste0(TRAINING_DIR, "results/report/02_Beta-diversity/")
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results_dir <- paste0(training_dir, "results/report/02_Beta-diversity/")
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dir.create(results_dir, recursive = TRUE, showWarnings = FALSE)
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```

‎tutorial/03_Abundance-overview_tutorial.Rmd‎

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Original file line numberDiff line numberDiff line change
@@ -72,19 +72,19 @@ library(RColorBrewer)
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**Load species abundance, taxonomical annotation and metadata file**
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```{r}
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TRAINING_DIR <- "/workspaces/dsp_metagenomics_training/"
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training_dir <- "/workspaces/dsp_metagenomics_training/"
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```
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```{r}
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# Abundance table
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abundance <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAbundance_Species.rds"))
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abundance <- readRDS(file = paste0(training_dir, "data/MetaphlanAbundance_Species.rds"))
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rownames(abundance) <- gsub("_SRR_db1.metaphlan", "", rownames(abundance))
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# Taxonomical annotation
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annotation <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAnnotations_Species.rds"))
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annotation <- readRDS(file = paste0(training_dir, "data/MetaphlanAnnotations_Species.rds"))
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# Metadata
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metadata <- read.table(file = paste0(TRAINING_DIR, "data/metadata.tsv"), header = TRUE,
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metadata <- read.table(file = paste0(training_dir, "data/metadata.tsv"), header = TRUE,
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sep = "\t",
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quote = "",
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row.names = NULL)
@@ -103,7 +103,7 @@ abundance <- abundance[rownames(abundance) %in%
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## Creating a directory for the related results
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```{r}
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results_dir <- paste0(TRAINING_DIR, "results/report/03_Abundance-overview/")
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results_dir <- paste0(training_dir, "results/report/03_Abundance-overview/")
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dir.create(results_dir,
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recursive = TRUE,

‎tutorial/04_Group-comparison_tutorial.Rmd‎

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Original file line numberDiff line numberDiff line change
@@ -74,19 +74,19 @@ library(FSA)
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**Load species abundance, taxonomical annotation and metadata file**
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```{r}
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TRAINING_DIR <- "/workspaces/dsp_metagenomics_training/"
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training_dir <- "/workspaces/dsp_metagenomics_training/"
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```
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```{r}
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# Abundance table
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abundance <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAbundance_Species.rds"))
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abundance <- readRDS(file = paste0(training_dir, "data/MetaphlanAbundance_Species.rds"))
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rownames(abundance) <- gsub("_SRR_db1.metaphlan", "", rownames(abundance))
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# Taxonomical annotation
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annotation <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAnnotations_Species.rds"))
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annotation <- readRDS(file = paste0(training_dir, "data/MetaphlanAnnotations_Species.rds"))
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# Metadata
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metadata <- read.table(file = paste0(TRAINING_DIR, "data/metadata.tsv"), header = TRUE,
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metadata <- read.table(file = paste0(training_dir, "data/metadata.tsv"), header = TRUE,
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sep = "\t",
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quote = "",
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row.names = NULL)
@@ -99,7 +99,7 @@ abundance <- abundance[rownames(metadata),]
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## Creating a directory for the related results
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```{r}
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results_dir <- paste0(TRAINING_DIR, "results/report/04_Group-comparison")
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results_dir <- paste0(training_dir, "results/report/04_Group-comparison")
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dir.create(results_dir, recursive = TRUE, showWarnings = FALSE)
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```

‎tutorial/05_Microb-networks_tutorial.Rmd‎

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Original file line numberDiff line numberDiff line change
@@ -76,21 +76,21 @@ library(dplyr)
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## Load data
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```{r}
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TRAINING_DIR <- "/workspaces/dsp_metagenomics_training/"
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training_dir <- "/workspaces/dsp_metagenomics_training/"
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```
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```{r, warning=FALSE}
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# Abundance table
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abundance <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAbundance_Species.rds"))
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abundance <- readRDS(file = paste0(training_dir, "data/MetaphlanAbundance_Species.rds"))
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rownames(abundance) <- gsub("_SRR_db1.metaphlan", "", rownames(abundance))
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dim(abundance)
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# Taxonomical annotation
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annotation <- readRDS(file = paste0(TRAINING_DIR, "data/MetaphlanAnnotations_Species.rds"))
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annotation <- readRDS(file = paste0(training_dir, "data/MetaphlanAnnotations_Species.rds"))
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dim(annotation)
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# Metadata
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metadata <- read.table(file = paste0(TRAINING_DIR, "data/metadata.tsv"), header = TRUE,
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metadata <- read.table(file = paste0(training_dir, "data/metadata.tsv"), header = TRUE,
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sep = "\t",
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quote = "",
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row.names = NULL)
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## Create a directory to store the results
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```{r, warning=FALSE}
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results_dir <- paste0(TRAINING_DIR, "results/report/05_Microbial-association-networks/")
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results_dir <- paste0(training_dir,
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"results/report/05_Microbial-association-networks/")
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dir.create(results_dir, recursive = TRUE, showWarnings = FALSE)
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```

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