Merge pull request #414 from ncborcherding/dev

update clonalLength()

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 = "[email protected]"), 
     person(given = "Qile", family = "Yang", role = c("aut"), email = "[email protected]"), 

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

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)
 

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)
 }