Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 48:d08dfc8d5225 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 27 Jan 2016 10:36:35 -0500 |
| parents | d97e1421aa86 |
| children | 188712b1735f |
| files | report_clonality/RScript.r report_clonality/r_wrapper.sh |
| diffstat | 2 files changed, 27 insertions(+), 13 deletions(-) [+] |
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--- a/report_clonality/RScript.r Wed Jan 27 10:25:43 2016 -0500 +++ b/report_clonality/RScript.r Wed Jan 27 10:36:35 2016 -0500 @@ -62,7 +62,9 @@ #filter uniques inputdata.removed = inputdata[NULL,] -if(filter_uniques == "yes" && c("CDR1.Seq", "CDR2.Seq", "CDR3.Seq", "FR1.IMGT", "FR2.IMGT", "FR3.IMGT") %in% names(inputdata)){ +filter_uniques = filter_uniques == "yes" && c("CDR1.Seq", "CDR2.Seq", "CDR3.Seq", "FR1.IMGT", "FR2.IMGT", "FR3.IMGT") %in% names(inputdata) + +if(filter_uniques){ clmns = names(inputdata) @@ -177,12 +179,17 @@ sample_productive_count$perc_unprod = round(sample_productive_count$Unproductive / sample_productive_count$All * 100) sample_productive_count$perc_unprod_un = round(sample_productive_count$Unproductive_unique / sample_productive_count$All * 100) -inputdata.removed.s = data.table(inputdata.removed)[, list(UniqueRemoved=.N), by=c("Sample")] + +if(filter_uniques){ + inputdata.removed.s = data.table(inputdata.removed)[, list(UniqueRemoved=.N), by=c("Sample")] + + sample_productive_count = merge(sample_productive_count, inputdata.removed.s, by="Sample") -sample_productive_count = merge(sample_productive_count, inputdata.removed.s, by="Sample") - -sample_productive_count$perc_rem = round(sample_productive_count$UniqueRemoved / sample_productive_count$All * 100) - + sample_productive_count$perc_rem = round(sample_productive_count$UniqueRemoved / sample_productive_count$All * 100) +} else { + sample_productive_count$UniqueRemoved = 0 + sample_productive_count$perc_rem = 0 +} sample_replicate_productive_count = inputdata.dt[, list(All=.N, Productive = nrow(.SD[.SD$Functionality == "productive" | .SD$Functionality == "productive (see comment)",]), @@ -201,12 +208,17 @@ sample_replicate_productive_count$perc_unprod = round(sample_replicate_productive_count$Unproductive / sample_replicate_productive_count$All * 100) sample_replicate_productive_count$perc_unprod_un = round(sample_replicate_productive_count$Unproductive_unique / sample_replicate_productive_count$All * 100) -inputdata.removed.sr = data.table(inputdata.removed)[, list(UniqueRemoved=.N), by=c("samples_replicates")] + +if(filter_uniques){ + inputdata.removed.sr = data.table(inputdata.removed)[, list(UniqueRemoved=.N), by=c("samples_replicates")] + + sample_replicate_productive_count = merge(sample_replicate_productive_count, inputdata.removed.sr, by="samples_replicates") -sample_replicate_productive_count = merge(sample_replicate_productive_count, inputdata.removed.sr, by="samples_replicates") - -sample_replicate_productive_count$perc_rem = round(sample_replicate_productive_count$UniqueRemoved / sample_productive_count$All * 100) - + sample_replicate_productive_count$perc_rem = round(sample_replicate_productive_count$UniqueRemoved / sample_productive_count$All * 100) +} else { + sample_replicate_productive_count$UniqueRemoved = 0 + sample_replicate_productive_count$perc_rem = 0 +} setnames(sample_replicate_productive_count, colnames(sample_productive_count))
--- a/report_clonality/r_wrapper.sh Wed Jan 27 10:25:43 2016 -0500 +++ b/report_clonality/r_wrapper.sh Wed Jan 27 10:36:35 2016 -0500 @@ -35,12 +35,14 @@ echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $2 echo "<table border = 1>" >> $2 -echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Removed</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2 +echo "<thead><tr><th>Sample/Replicate</th><th>Input</th><th>Removed</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un removed perc_rem do echo "<tr><td>$sample</td>" >> $2 + + echo "<td>$((all+removed))</td>" >> $2 + echo "<td>${removed} (${perc_rem}%)</td>" >> $2 echo "<td>$all</td>" >> $2 - echo "<td>${removed} (${perc_rem}%)</td>" >> $2 echo "<td>$productive (${perc_prod}%)</td>" >> $2 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2