comparison RScript.r @ 56:c89d9e89423b draft

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55:43ce3ebfc9b5

single_patients = data.frame("Patient" = character(0),"Sample" = character(0), "on" = character(0), "Clone_Sequence" = character(0), "Frequency" = numeric(0), "normalized_read_count" = numeric(0), "V_Segment_Major_Gene" = character(0), "J_Segment_Major_Gene" = character(0), "Rearrangement" = character(0))

patient.merge.list = list() #cache the 'both' table, 2x speedup for more memory...
patient.merge.list.second = list()
cat(paste("<table border='0'>", sep=""), file="multiple_matches.html", append=T)
patientCountOnColumn <- function(x, product, interval, on, appendtxt=F){
  if (!is.data.frame(x) & is.list(x)){
    x = x[[1]]
  }
  #x$Sample = factor(x$Sample, levels=unique(x$Sample))

        patient.fuzzy = patient.fuzzy[!(first.match.filter | second.match.filter),]

        hidden.clone.sequences = c(first.rows[-1,"Clone_Sequence"], second.rows[second.rows$Clone_Sequence != first.clone.sequence,"Clone_Sequence"])
        merge.list[["second"]] = append(merge.list[["second"]], hidden.clone.sequences)

        if(sum(first.match.filter) == 1 & sum(second.match.filter) == 1){
          second.clone.sequence = patient.fuzzy[second.match.filter, "Clone_Sequence"]
          if(first.clone.sequence != second.clone.sequence){
            #merge.list[["second"]] = append(merge.list[["second"]], second.clone.sequence)
          }
        }

        if(nrow(first.rows) > 1 | nrow(second.rows) > 1){
          cat(paste("<tr><td>", patient, ": ", nrow(first.rows), " ", nrow(second.rows), " ", first.clone.sequence,  "</td></tr>", sep=""), file="multiple_matches.html", append=T)
        }

      } else {
        patient.fuzzy = patient.fuzzy[-1,]
      }

56:c89d9e89423b

single_patients = data.frame("Patient" = character(0),"Sample" = character(0), "on" = character(0), "Clone_Sequence" = character(0), "Frequency" = numeric(0), "normalized_read_count" = numeric(0), "V_Segment_Major_Gene" = character(0), "J_Segment_Major_Gene" = character(0), "Rearrangement" = character(0))

patient.merge.list = list() #cache the 'both' table, 2x speedup for more memory...
patient.merge.list.second = list()
cat(paste("<table border='0' style='font-family:courier;'>", sep=""), file="multiple_matches.html", append=T)
cat(paste("<table border='0' style='font-family:courier;'>", sep=""), file="single_matches.html", append=T)
patientCountOnColumn <- function(x, product, interval, on, appendtxt=F){
  if (!is.data.frame(x) & is.list(x)){
    x = x[[1]]
  }
  #x$Sample = factor(x$Sample, levels=unique(x$Sample))

        patient.fuzzy = patient.fuzzy[!(first.match.filter | second.match.filter),]

        hidden.clone.sequences = c(first.rows[-1,"Clone_Sequence"], second.rows[second.rows$Clone_Sequence != first.clone.sequence,"Clone_Sequence"])
        merge.list[["second"]] = append(merge.list[["second"]], hidden.clone.sequences)

        tmp.rows = rbind(first.rows, second.rows)
        tmp.rows = tmp.rows[order(nchar(tmp.rows$Clone_Sequence)),]

        if (nrow(first.rows) > 1 | nrow(second.rows) > 1) {
          cat(paste("<tr><td>", patient, " row ", 1:nrow(tmp.rows), "</td><td>", tmp.rows$Sample, ":</td><td>", tmp.rows$Clone_Sequence, "</td><td>", tmp.rows$normalized_read_count, "</td></tr>", sep=""), file="multiple_matches.html", append=T)
        } else {
          second.clone.sequence = second.rows[1,"Clone_Sequence"]
          if(nchar(first.clone.sequence) != nchar(second.clone.sequence)){
            cat(paste("<tr bgcolor='#DDD'><td>", patient, " row ", 1:nrow(tmp.rows), "</td><td>", tmp.rows$Sample, ":</td><td>", tmp.rows$Clone_Sequence, "</td><td>", tmp.rows$normalized_read_count, "</td></tr>", sep=""), file="single_matches.html", append=T)
          } else {
            cat(paste("<tr><td>", patient, " row ", 1:nrow(tmp.rows), "</td><td>", tmp.rows$Sample, ":</td><td>", tmp.rows$Clone_Sequence, "</td><td>", tmp.rows$normalized_read_count, "</td></tr>", sep=""), file="single_matches.html", append=T)
          }
        }

      } else {
        patient.fuzzy = patient.fuzzy[-1,]
      }