From 21e3b54aaaf434c33142f941b2169f3a612c9727 Mon Sep 17 00:00:00 2001
From: theHumanBorch <ncborch@gmail.com>
Date: Tue, 8 Oct 2024 12:36:10 -0500
Subject: [PATCH] update clonalLength()

Fix issue with single chain per #412
Removed code that was pre-data.wrangle() internal function
---
 DESCRIPTION      |  2 +-
 NEWS.md          |  6 ++++++
 R/clonalLength.R | 13 +------------
 R/utils.R        | 11 +++++++----
 4 files changed, 15 insertions(+), 17 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fa2d7193..e4453f48 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: scRepertoire
 Title: A toolkit for single-cell immune receptor profiling
-Version: 2.0.7
+Version: 2.0.8
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"), 
     person(given = "Qile", family = "Yang", role = c("aut"), email = "qile.yang@berkeley.edu"), 
diff --git a/NEWS.md b/NEWS.md
index bcf67b14..e262e8d7 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# scRepertoire VERSION 2.0.8
+
+## UNDERLYING CHANGES
+* Fixed issue with single chain output for ```clonalLength()```
+* Removed unnecessary code remnant in ```clonalLength()```
+
 # scRepertoire VERSION 2.0.7
 
 ## UNDERLYING CHANGES
diff --git a/R/clonalLength.R b/R/clonalLength.R
index b5314279..a1817c3b 100644
--- a/R/clonalLength.R
+++ b/R/clonalLength.R
@@ -61,20 +61,9 @@ clonalLength <- function(input.data,
           CDR3 sequence to analyze by using `cloneCall`")
   }
   
-  #Identifying and assigning chains
-  chain.pos <- which(colnames(input.data[[1]]) == "cdr3_aa1")-1
-  c1 <- na.omit(unique(substr(input.data[[1]][seq_len(10),chain.pos], 1,3)))
-  c1 <- c1[c1 != "NA."]
-  c1 <- c1[c1 != "NA"]
-
-  c2 <- switch(c1,
-               "TRA" = "TRB",
-               "IGH"  = "IGL",
-               "TRG"  = "TRD")
-  
   #Calculating Length
   Con.df <- NULL
-  Con.df <- .lengthDF(input.data, cloneCall, chain, group.by, c1, c2)
+  Con.df <- .lengthDF(input.data, cloneCall, chain, group.by)
   
   names <- names(input.data)
   
diff --git a/R/utils.R b/R/utils.R
index a6a86185..75bd06f7 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -427,7 +427,7 @@
 #Producing a data frame to visualize for lengthContig()
 #' @keywords internal
 #' @importFrom stringr str_remove_all
-.lengthDF <- function(df, cloneCall, chain, group, c1, c2){
+.lengthDF <- function(df, cloneCall, chain, group){
     Con.df <- NULL
     names <- names(df)
     if (identical(chain, "both")) {
@@ -456,14 +456,17 @@
                 chain1 <- nchar(val1)
                 if (!is.null(group)) {
                     cols1 <- df[[x]][,group]
-                    data1 <- data.frame(chain1, val1, names[x], c1, cols1)
+                    data1 <- data.frame(chain1, val1, names[x], chain, cols1)
                     colnames(data1)<-c("length","CT","values","chain",group)
                 }else if (is.null(group)){
-                    data1 <- data.frame(chain1, val1, names[x], c1)
+                    data1 <- data.frame(chain1, val1, names[x], chain)
                     colnames(data1) <- c("length", "CT", "values", "chain")
+                }
                 data <- na.omit(data1)
                 data <- subset(data, CT != "NA" & CT != "")
-                Con.df<- rbind.data.frame(Con.df, data) }}
+                Con.df<- rbind.data.frame(Con.df, data) 
+                
+            }
     }
     return(Con.df)
 }