remove tidyverse

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)
 

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)
 

bin/plot_pairwise.R

@@ -1,4 +1,7 @@
-library(tidyverse)
+# library(tidyverse)
+library(dplyr)
+library(readr)
+library(stringr)
 library(ggplot2)
 
 args <- commandArgs(trailingOnly=TRUE)

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) {

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)

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)
 

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"))