Deleted R here package usage

nasa · Nov 15, 2024 · 1dbfe66 · 1dbfe66
1 parent 57b5bc0
commit 1dbfe66
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Showing 6 changed files with 24 additions and 24 deletions.
diff --git a/...icon/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/alpha_diversity.R b/...icon/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/alpha_diversity.R
@@ -210,10 +210,10 @@ custom_palette <- custom_palette[-c(21:23, grep(pattern = pattern_to_filter,
 
 
 # Required variables
-metadata_file <- here(opt[["metadata-table"]]) 
-features_file <- here(opt[["feature-table"]])
-taxonomy_file <- here(opt[["taxonomy-table"]])
-alpha_diversity_out_dir <- here("alpha_diversity/")
+metadata_file <- opt[["metadata-table"]] 
+features_file <- opt[["feature-table"]]
+taxonomy_file <- opt[["taxonomy-table"]]
+alpha_diversity_out_dir <-"alpha_diversity/"
 if(!dir.exists(alpha_diversity_out_dir)) dir.create(alpha_diversity_out_dir)
 # Metadata group column name to compare
 groups_colname <- opt[["group"]]

diff --git a/Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/beta_diversity.R b/Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/beta_diversity.R
@@ -221,10 +221,10 @@ custom_palette <- custom_palette[-c(21:23, grep(pattern = pattern_to_filter,
 # 2. Add rarefaction
 
 # Required variables
-metadata_file <- here(opt[["metadata-table"]])
-features_file <-  here(opt[["feature-table"]]) 
-taxonomy_file <-  here(opt[["taxonomy-table"]])
-beta_diversity_out_dir <- here("beta_diversity/")
+metadata_file <- opt[["metadata-table"]]
+features_file <-  opt[["feature-table"]] 
+taxonomy_file <-  opt[["taxonomy-table"]]
+beta_diversity_out_dir <- "beta_diversity/"
 if(!dir.exists(beta_diversity_out_dir)) dir.create(beta_diversity_out_dir)
 # Metadata group column name to compare
 groups_colname <- opt[["group"]]

diff --git a/...on/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/pairwise_ancombc1.R b/...on/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/pairwise_ancombc1.R
@@ -290,9 +290,9 @@ publication_format <- theme_bw() +
 group <- opt[["group"]]  # "groups"
 samples_column <- opt[["samples-column"]] # "Sample Name"
 threads <- opt[["cpus"]] # 8
-metadata_file <- here(opt[["metadata-table"]])
-taxonomy_file <-  here(opt[["taxonomy-table"]])
-feature_table_file <- here(opt[["feature-table"]]) 
+metadata_file <- opt[["metadata-table"]]
+taxonomy_file <-  opt[["taxonomy-table"]]
+feature_table_file <- opt[["feature-table"]]
 feature <- opt[["feature-type"]]   # "ASV"
 output_prefix <- opt[["output-prefix"]]
 assay_suffix <- opt[["assay-suffix"]]
@@ -301,7 +301,7 @@ assay_suffix <- opt[["assay-suffix"]]
 prevalence_cutoff <- opt[["prevalence-cutoff"]] # 0.15 (15%)
 # sample / library read count cutoff
 library_cutoff <- opt[["library-cutoff"]]  # 100
-diff_abund_out_dir <- here("differential_abundance/")
+diff_abund_out_dir <- "differential_abundance/"
 if(!dir.exists(diff_abund_out_dir)) dir.create(diff_abund_out_dir)
 
 

diff --git a/...on/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/pairwise_ancombc2.R b/...on/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/pairwise_ancombc2.R
@@ -346,9 +346,9 @@ publication_format <- theme_bw() +
 group <- opt[["group"]]  # "groups"
 samples_column <- opt[["samples-column"]] # "Sample Name"
 threads <- opt[["cpus"]] # 8
-metadata_file <- here(opt[["metadata-table"]])
-taxonomy_file <-  here(opt[["taxonomy-table"]])
-feature_table_file <- here(opt[["feature-table"]]) 
+metadata_file <- opt[["metadata-table"]]
+taxonomy_file <-  opt[["taxonomy-table"]]
+feature_table_file <- opt[["feature-table"]]
 feature <- opt[["feature-type"]]   # "ASV"
 output_prefix <- opt[["output-prefix"]]
 assay_suffix <- opt[["assay-suffix"]]
@@ -357,7 +357,7 @@ assay_suffix <- opt[["assay-suffix"]]
 prevalence_cutoff <- opt[["prevalence-cutoff"]] # 0.15 (15%)
 # sample / library read count cutoff
 library_cutoff <- opt[["library-cutoff"]]  # 100
-diff_abund_out_dir <- here("differential_abundance/")
+diff_abund_out_dir <- "differential_abundance/"
 if(!dir.exists(diff_abund_out_dir)) dir.create(diff_abund_out_dir)
 
 # ------------------------ Read metadata ---------------------------------- #

diff --git a/Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/plot_taxonomy.R b/Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/plot_taxonomy.R
@@ -361,10 +361,10 @@ custom_palette <- custom_palette[-c(21:23, grep(pattern = pattern_to_filter,
 
 
 # Required variables
-metadata_file <- here(opt[["metadata-table"]]) 
-features_file <- here(opt[["feature-table"]])
-taxonomy_file <- here(opt[["taxonomy-table"]])
-taxonomy_plots_out_dir <- here("taxonomy_plots/")
+metadata_file <- opt[["metadata-table"]]
+features_file <- opt[["feature-table"]]
+taxonomy_file <- opt[["taxonomy-table"]]
+taxonomy_plots_out_dir <- "taxonomy_plots/"
 if(!dir.exists(taxonomy_plots_out_dir)) dir.create(taxonomy_plots_out_dir)
 # Metadata group column name to compare
 groups_colname <- opt[["group"]]

diff --git a/Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/run_deseq2.R b/Amplicon/Illumina/Workflow_Documentation/NF_AmpIllumina-B/workflow_code/bin/run_deseq2.R
@@ -130,9 +130,9 @@ library(DESeq2)
 group <- opt[["group"]]  # "groups"
 samples_column <- opt[["samples-column"]] # "Sample Name"
 threads <- opt[["cpus"]] # 8
-metadata_file <- here(opt[["metadata-table"]])
-taxonomy_file <-  here(opt[["taxonomy-table"]])
-feature_table_file <- here(opt[["feature-table"]]) 
+metadata_file <- opt[["metadata-table"]]
+taxonomy_file <-  opt[["taxonomy-table"]]
+feature_table_file <- opt[["feature-table"]]
 feature <- opt[["feature-type"]]   # "ASV"
 output_prefix <- opt[["output-prefix"]]
 assay_suffix <- opt[["assay-suffix"]]
@@ -141,7 +141,7 @@ assay_suffix <- opt[["assay-suffix"]]
 prevalence_cutoff <- opt[["prevalence-cutoff"]] # 0.15 (15%)
 # sample / library read count cutoff
 library_cutoff <- opt[["library-cutoff"]]  # 100
-diff_abund_out_dir <- here("differential_abundance/")
+diff_abund_out_dir <- "differential_abundance/"
 if(!dir.exists(diff_abund_out_dir)) dir.create(diff_abund_out_dir)