From 3868a48a58f154dbd50f40bb314495bfaf448df2 Mon Sep 17 00:00:00 2001
From: kwells4 <kristen.wells@cuanschutz.edu>
Date: Fri, 12 May 2023 11:00:39 -0600
Subject: [PATCH 1/3] making compatable with older versions of dplyr

---
 R/import-vdj.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/import-vdj.R b/R/import-vdj.R
index a0b7ba2b..2b2a7184 100644
--- a/R/import-vdj.R
+++ b/R/import-vdj.R
@@ -963,8 +963,7 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
   # left_join + mutate is much faster than valr::bed_intersect, probably due
   # to the extreme number of "chromosomes"
   vdj_muts <- dplyr::left_join(
-    mut_coords, vdj_coords, by = "contig_id", suffix = c("", ".seg"),
-    relationship = "many-to-many"
+    mut_coords, vdj_coords, by = "contig_id", suffix = c("", ".seg")
   )
 
   vdj_muts <- dplyr::filter(

From 839a92a3e28e575968ff7edff22391708fc296b4 Mon Sep 17 00:00:00 2001
From: kwells4 <kristen.wells@cuanschutz.edu>
Date: Fri, 16 Jun 2023 17:02:59 -0600
Subject: [PATCH 2/3] fixing relationship argument to be dependent on dplyr
 version

---
 R/import-vdj.R | 27 +++++++++++++++++----------
 1 file changed, 17 insertions(+), 10 deletions(-)

diff --git a/R/import-vdj.R b/R/import-vdj.R
index a0b7ba2b..3033d31f 100644
--- a/R/import-vdj.R
+++ b/R/import-vdj.R
@@ -932,11 +932,11 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
 
   # Get the full length sequence of the vdj region with and without c region
   vdj_coords <- vdj_coords %>%
-    dplyr::mutate(new_len = ifelse(seg == "c", 0, len)) %>%
-    dplyr::group_by(contig_id) %>%
-    dplyr::mutate(full_len = sum(len),
-                  full_len_vdj = sum(new_len)) %>%
-    dplyr::select(!new_len)
+    dplyr::mutate(new_len = ifelse(.data$seg == "c", 0, .data$len)) %>%
+    dplyr::group_by(.data$contig_id) %>%
+    dplyr::mutate(full_len = sum(.data$len),
+                  full_len_vdj = sum(.data$new_len)) %>%
+    dplyr::select(!"new_len")
   
   mut_coords <- dplyr::mutate(
     mut_coords,
@@ -962,10 +962,17 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
   # some annotations overlap each other! Example: AAACCTGAGAACTGTA-1_contig_1
   # left_join + mutate is much faster than valr::bed_intersect, probably due
   # to the extreme number of "chromosomes"
-  vdj_muts <- dplyr::left_join(
-    mut_coords, vdj_coords, by = "contig_id", suffix = c("", ".seg"),
-    relationship = "many-to-many"
-  )
+  if (utils::packageVersion("dplyr") > "1.1.1") { 
+    # relationship argument gained in 1.1.1 https://dplyr.tidyverse.org/news/index.html
+    vdj_muts <- dplyr::left_join(
+      mut_coords, vdj_coords, by = "contig_id", suffix = c("", ".seg"),
+      relationship = "many-to-many"
+    )
+  } else {
+    vdj_muts <- dplyr::left_join(
+        mut_coords, vdj_coords, by = "contig_id", suffix = c("", ".seg")
+        )
+  }
 
   vdj_muts <- dplyr::filter(
     vdj_muts, .data$start < .data$end.seg & .data$end > .data$start.seg
@@ -1028,7 +1035,7 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
     sum_column <- "full_len"
   } else {
     all_muts <- all_muts %>%
-      dplyr::filter(seg != "c")
+      dplyr::filter(.data$seg != "c")
     sum_column <- "full_len_vdj"
   }
   

From f76c26b535c17bd38f960968cb13c05c2d27d4fe Mon Sep 17 00:00:00 2001
From: Ryan Sheridan <ryan.sheridan@cuanschutz.edu>
Date: Mon, 19 Jun 2023 10:46:59 -0600
Subject: [PATCH 3/3] fix test warnings

---
 R/calc-gene-usage.R | 2 +-
 R/import-vdj.R      | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/calc-gene-usage.R b/R/calc-gene-usage.R
index 356d6b4e..12b6ebc9 100644
--- a/R/calc-gene-usage.R
+++ b/R/calc-gene-usage.R
@@ -659,7 +659,7 @@ plot_gene_pairs <- function(input, data_col, chains, cluster_col = NULL,
   n_lab_dat$legend <- n_lab_dat$axis <- n_lab_dat$corner
 
   if ((!is.null(grp_col) || !is.null(clst_col)) && identical(method, "bar")) {
-    n_lab_dat$axis <- dplyr::rename(df_in, .n = .data$freq)
+    n_lab_dat$axis <- dplyr::rename(df_in, .n = "freq")
   }
 
   # Set common arguments
diff --git a/R/import-vdj.R b/R/import-vdj.R
index 3033d31f..af7400c4 100644
--- a/R/import-vdj.R
+++ b/R/import-vdj.R
@@ -313,7 +313,7 @@ import_vdj <- function(input = NULL, vdj_dir = NULL, prefix = "",
       # contigs that did not have any mutations will have NAs
       indel_ctigs <- purrr::map(
         indel_ctigs,
-        ~ mutate(.x, dplyr::across(all_of(indel_cols), tidyr::replace_na, 0))
+        ~ mutate(.x, dplyr::across(all_of(indel_cols), ~ tidyr::replace_na(.x, 0)))
       )
 
       contigs    <- indel_ctigs