tempo data prep for circos

bin/circos.R

@@ -4,8 +4,8 @@ sheetName <- "mouse_1" # sheet number
 Name <- "Name" # column of the sequence names
 col1 <- "VH_VJ" # first column name
 col2 <- "VL_VJ" # second column name
-col1.selection <- "IGHV1-55_IGHJ2" # single vector of characters indicating the values to select inside col1 for the circos representation. Write NULL if not required
-col2.selection <- "IGKV4-68_IGKJ5" # single vector of characters indicating the values to select inside col2 for the circos representation. Write NULL if not required
+col1.selection <- c("IGHV1-7_IGHJ2", "IGHV1-55_IGHJ2", "IGHV1-81_IGHJ2") # single vector of characters indicating the values to select inside col1 for the circos representation. Write NULL if not required
+col2.selection <- c("IGKV4-68_IGKJ5", "IGKV2-112_IGKJ2") # single vector of characters indicating the values to select inside col2 for the circos representation. Write NULL if not required
 metadata <- c("mAb_name", "Kd_nM") # single vector of characters indicating the name of the column with metadata
 scale.size <- 0.7 # size of the numbers
 label.size <- 0.7 # size of the label text

bin/circos_data_prep.R

+erase.objects = TRUE # write TRUE to erase all the existing objects in R before starting the algorithm and FALSE otherwise. Beginners should use TRUE
+if(erase.objects == TRUE){
+    rm(list = ls(all.names = TRUE))
+    erase.objects = TRUE
+}
+erase.graphs = TRUE # write TRUE to erase all the graphic windows in R before starting the algorithm and FALSE otherwise
+script <- "circos_data_prep"
+
+VH.path <- "X:/ROCURONIUM PROJECT/01 Primary data/04.Repertoire analysis/SORT1/SORT1 Seq-original/RESULT/repertoire_profiler_1708127835/all_passed_seq.tsv" # Must be VH
+VL.path <- "X:/ROCURONIUM PROJECT/01 Primary data/04.Repertoire analysis/SORT1/SORT1 Seq-original/RESULT/repertoire_profiler_1708128192/all_passed_seq.tsv" # must be VL
+merging_colums_names <- c("initial_sequence_id") # single vector of character strings of the names of the column used to merge the 2 files. Of note, if _VH or _VL in the columns names, they are removed.
+metadata_colums_names <- c("sequence_id") # single character string of the name of the metadata column in the two files. Write NULL if no metadata.
+kept_colums_names <- c("germline_v_call",	"germline_j_call") # single vector of character strings of the names of the column of VH.path file that correspond to V (first position) and J. Of note, Same names must be for VH and VL.
+
+
+
+df1 <- read.table(VH.path, sep = "\t", header = TRUE)
+df2 <- read.table(VL.path, sep = "\t", header = TRUE)
+if( ! all(merging_colums_names %in% names(df1))){
+    stop("ERROR 1")
+}
+if( ! all(merging_colums_names %in% names(df2))){
+    stop("ERROR 2")
+}
+if( ! all(kept_colums_names %in% names(df1))){
+    stop("ERROR 3")
+}
+if( ! all(kept_colums_names %in% names(df2))){
+    stop("ERROR 4")
+}
+if(any(duplicated(df1[ , merging_colums_names]))){
+    stop("ERROR 5")
+}
+if(any(duplicated(df2[ , merging_colums_names]))){
+    stop("ERROR 6")
+}
+
+# removal of _VH and _VL in these columns
+df1[ , merging_colums_names] <- gsub(df1[ , merging_colums_names], pattern = "_VH", replacement = "")
+df2[ , merging_colums_names] <- gsub(df2[ , merging_colums_names], pattern = "_VL", replacement = "")
+df1[ , metadata_colums_names] <- gsub(df1[ , metadata_colums_names], pattern = "_VH", replacement = "")
+df2[ , metadata_colums_names] <- gsub(df2[ , metadata_colums_names], pattern = "_VL", replacement = "")
+# end removal of _VH and _VL in these columns
+
+# columns rename before merging
+renamed_colums_names <- c("V_allele", "J_allele") # single vector of character strings of the names of VH.path file to keep, beyond metadata. Of note, Same names must be for VH and VL.
+names(df1)[match(kept_colums_names, names(df1))] <- paste0(renamed_colums_names, "_VH")
+names(df1)[match(metadata_colums_names, names(df1))] <- "Metadata_VH"
+names(df2)[match(kept_colums_names, names(df2))] <- paste0(renamed_colums_names, "_VL")
+names(df2)[match(metadata_colums_names, names(df2))] <- "Metadata_VL"
+# end columns rename before merging
+
+# selection of the columns of interest
+df1 <- df1[ , c(merging_colums_names,"Metadata_VH", paste0(renamed_colums_names, "_VH"))]
+df2 <- df2[ , c(merging_colums_names, "Metadata_VL", paste0(renamed_colums_names, "_VL"))]
+# end selection of the columns of interest
+
+# merging
+tempo.log1 <- is.na(match(df1[ , merging_colums_names], df2[ , merging_colums_names]))
+tempo.log2 <- is.na(match(df2[ , merging_colums_names], df1[ , merging_colums_names]))
+if(any(tempo.log1)){
+    cat(paste0("\n\nWarning: SOME SEQUENCES FROM VH ARE REMOVED BECAUSE NOT IN THE OTHER VL FILE:\n", paste(df1[ , merging_colums_names][tempo.log1], collapse = "\n"), "\n\n"))
+}
+if(any(tempo.log2)){
+    cat(paste0("\n\nWarning: SOME SEQUENCES FROM VL ARE REMOVED BECAUSE NOT IN THE OTHER VH FILE:\n", paste(df2[ , merging_colums_names][tempo.log2], collapse = "\n"), "\n\n"))
+}
+df1 <- df1[ ! tempo.log1, ]
+df2 <- df2[ ! tempo.log2, ]
+nrow(df1)
+nrow(df2)
+identical(sort(df1[ , merging_colums_names]), sort(df2[ , merging_colums_names]))
+output_all_seq <- merge(df1, df2, by = c("initial_sequence_id"), sort = FALSE) # rd for random. Send the coord of the boxes into the coord data.frame of the dots (in the column x.y). WARNING: by = c("PANEL", "group") without fill column because PANEL & group columns are enough as only one value of x column per group number in box.coord. Thus, no need to consider fill column
+nrow(output_all_seq)
+if(nrow(output_all_seq) != nrow(df1)){
+    tempo.cat <- paste0("INTERNAL CODE ERROR. THE merge() FUNCTION DID NOT RETURN A CORRECT output DATA FRAME. CODE HAS TO BE MODIFIED")
+    stop(paste0("\n\n================\n\n", tempo.cat, "\n\n================\n\n", call. = FALSE)) # == in stop() to be able to add several messages between ==
+}
+# end merging
+
+# new columns wo * in alleles
+output_all_seq <- data.frame(
+    output_all_seq, 
+    V_VH = (output_all_seq$V_allele_VH)
+)
+# end new columns wo * in alleles
+
+
+# new fusion columns
+output_all_seq <- data.frame(
+    output_all_seq, )
+# end new fusion columns
+
+# metadata in output_all_seq
+if( ! all(output_all_seq$Metadata_VH == output_all_seq$Metadata_VL)){
+    stop("ERROR 7")
+}
+output_all_seq <- output_all_seq[ , names(output_all_seq) != "Metadata_VL"] # removal of Metadata_VL
+names(output_all_seq)[names(output_all_seq) == "Metadata_VH"] <- "Metadata" # remane Metadata_VH into Metadata
+tempo.log <- is.na(match(output_all_seq[ , merging_colums_names], output_all_seq$Metadata)) # detection of the Metadata names
+output_all_seq$Metadata[ ! tempo.log] <- NA # keep only the Metadata names in the Metadata column
+# end metadata in output_all_seq
+
+# export output_all_seq
+
+# end export output_all_seq