From 205be40274f8706eda8786812776a30e39a90a17 Mon Sep 17 00:00:00 2001
From: katiesevans <kathrynevans2015@u.northwestern.edu>
Date: Mon, 7 Mar 2022 12:59:47 -0600
Subject: [PATCH] remove tidyverse

---
 bin/fq_concordance.R               | 5 ++++-
 bin/merge_groups_info.R            | 5 ++++-
 bin/plot_pairwise.R                | 5 ++++-
 bin/process_concordance.R          | 5 ++++-
 bin/process_concordance_report.Rmd | 6 +++++-
 bin/process_strain_pairwise.R      | 5 ++++-
 bin/process_trees.R                | 4 +++-
 7 files changed, 28 insertions(+), 7 deletions(-)

diff --git a/bin/fq_concordance.R b/bin/fq_concordance.R
index e809597..e59b3de 100644
--- a/bin/fq_concordance.R
+++ b/bin/fq_concordance.R
@@ -1,4 +1,7 @@
-library(tidyverse)
+# library(tidyverse)
+library(dplyr)
+library(readr)
+library(tidyr)
 
 gt_dict = list("0/0" = 0, "1/1" = 1)
 
diff --git a/bin/merge_groups_info.R b/bin/merge_groups_info.R
index 9cbf87b..47e8456 100644
--- a/bin/merge_groups_info.R
+++ b/bin/merge_groups_info.R
@@ -1,5 +1,8 @@
 #!/usr/bin/env Rscript
-library(tidyverse)
+# library(tidyverse)
+library(readr)
+library(dplyr)
+library(tidyr)
 # Read data from Rscript input
 args <- commandArgs(trailingOnly=TRUE)
 
diff --git a/bin/plot_pairwise.R b/bin/plot_pairwise.R
index 2f53a60..87332d9 100644
--- a/bin/plot_pairwise.R
+++ b/bin/plot_pairwise.R
@@ -1,4 +1,7 @@
-library(tidyverse)
+# library(tidyverse)
+library(dplyr)
+library(readr)
+library(stringr)
 library(ggplot2)
 
 args <- commandArgs(trailingOnly=TRUE)
diff --git a/bin/process_concordance.R b/bin/process_concordance.R
index c7283c3..eb65ace 100644
--- a/bin/process_concordance.R
+++ b/bin/process_concordance.R
@@ -1,6 +1,9 @@
 #!/usr/bin/env Rscript
 library(ggplot2)
-library(tidyverse)
+library(dplyr)
+library(readr)
+library(tidyr)
+# library(tidyverse)
 
 # Used in calculating isotypes
 stack_list <- function(x) {
diff --git a/bin/process_concordance_report.Rmd b/bin/process_concordance_report.Rmd
index 70b6119..bb8000a 100644
--- a/bin/process_concordance_report.Rmd
+++ b/bin/process_concordance_report.Rmd
@@ -18,7 +18,11 @@ output: html_document
 ```{r global_options, include=FALSE}
 knitr::opts_chunk$set(warning=FALSE, message=FALSE, echo=FALSE)
 
-library(tidyverse)
+# library(tidyverse)
+library(ggplot2)
+library(dplyr)
+library(readr)
+library(tidyr)
 library(magrittr)
 library(DT)
 library(plotly)
diff --git a/bin/process_strain_pairwise.R b/bin/process_strain_pairwise.R
index 66e11ea..0efa7c8 100644
--- a/bin/process_strain_pairwise.R
+++ b/bin/process_strain_pairwise.R
@@ -1,6 +1,9 @@
 #!/usr/bin/env Rscript
 library(ggplot2)
-library(tidyverse)
+library(readr)
+library(dplyr)
+library(tidyr)
+# library(tidyverse)
 # Read data from Rscript input
 args <- commandArgs(trailingOnly=TRUE)
 
diff --git a/bin/process_trees.R b/bin/process_trees.R
index 0ccc01d..3b2c991 100644
--- a/bin/process_trees.R
+++ b/bin/process_trees.R
@@ -1,7 +1,9 @@
 library(ape)
 library(ggmap)
 library(phyloseq)
-library(tidyverse)
+library(dplyr)
+library(ggplot2)
+# library(tidyverse)
 
 contig = commandArgs(trailingOnly=TRUE)[[1]]
 tree <- ape::read.tree(paste0(contig,".tree"))