| Previous changeset 2:e85fec274cde (2016-10-27) Next changeset 4:477e95b098fd (2016-10-31) |
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modified:
merge_and_filter.r shm_csr.py shm_csr.r wrapper.sh |
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| diff -r e85fec274cde -r 275ab5175fd6 merge_and_filter.r --- a/merge_and_filter.r Thu Oct 27 07:26:45 2016 -0400 +++ b/merge_and_filter.r Thu Oct 27 09:40:45 2016 -0400 |
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| @@ -194,6 +194,10 @@ result[!higher_than,"best_match"] = paste("unmatched,", result[!higher_than,"best_match"]) } +if(class.filter == "101_101"){ + result$best_match = "all" +} + if(any(higher_than, na.rm=T)){ #summ = summ[higher_than,] } |
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| diff -r e85fec274cde -r 275ab5175fd6 shm_csr.py --- a/shm_csr.py Thu Oct 27 07:26:45 2016 -0400 +++ b/shm_csr.py Thu Oct 27 09:40:45 2016 -0400 |
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| @@ -85,7 +85,7 @@ AALength = 64 AA_mutation = [0] * AALength -AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "unm": AA_mutation[:]} +AA_mutation_dic = {"IGA": AA_mutation[:], "IGG": AA_mutation[:], "IGM": AA_mutation[:], "unm": AA_mutation[:], "all": AA_mutation[:]} AA_mutation_empty = AA_mutation[:] aa_mutations_by_id_file = outfile[:outfile.rindex("/")] + "/aa_id_mutations.txt" |
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| diff -r e85fec274cde -r 275ab5175fd6 shm_csr.r --- a/shm_csr.r Thu Oct 27 07:26:45 2016 -0400 +++ b/shm_csr.r Thu Oct 27 09:40:45 2016 -0400 |
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| @@ -414,8 +414,8 @@ p = ggplot(dat.clss, aes(best_match, percentage_mutations)) p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA) p = p + xlab("Subclass") + ylab("Frequency") + ggtitle("Frequency scatter plot") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) -p = p + scale_fill_manual(values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet")) -p = p + scale_colour_manual(values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet")) +p = p + scale_fill_manual(values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet", "all" = "blue4")) +p = p + scale_colour_manual(values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet", "all" = "blue4")) png(filename="scatter.png") print(p) @@ -441,7 +441,7 @@ p = ggplot(frequency_bins_data, aes(frequency_bins, frequency)) p = p + geom_bar(aes(fill=best_match_class), stat="identity", position="dodge") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) -p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") + scale_fill_manual(values=c("IGA" = "blue4", "IGG" = "olivedrab3", "IGM" = "black")) +p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") + scale_fill_manual(values=c("IGA" = "blue4", "IGG" = "olivedrab3", "IGM" = "black", "all" = "blue4")) png(filename="frequency_ranges.png") print(p) |
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| diff -r e85fec274cde -r 275ab5175fd6 wrapper.sh --- a/wrapper.sh Thu Oct 27 07:26:45 2016 -0400 +++ b/wrapper.sh Thu Oct 27 09:40:45 2016 -0400 |
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| @@ -260,17 +260,17 @@ done < $outdir/data_${func}.txt else - tmp=`cat $outdir/unmatched_${func}_n.txt` + tmp=`cat $outdir/all_${func}_n.txt` echo "<th><a href='matched_all_${func}.txt'>all (N = $tmp)</a></th>" >> $output while IFS=, read name cax cay caz ca1x ca1y ca1z ca2x ca2y ca2z cgx cgy cgz cg1x cg1y cg1z cg2x cg2y cg2z cg3x cg3y cg3z cg4x cg4y cg4z cmx cmy cmz unx uny unz allx ally allz do if [ "$name" == "FR R/S (ratio)" ] || [ "$name" == "CDR R/S (ratio)" ] ; then #meh - echo "<tr><td>$name</td><td>${unx}/${uny}</td></tr>" >> $output + echo "<tr><td>$name</td><td>${allx}/${ally}</td></tr>" >> $output elif [ "$name" == "Median of Number of Mutations (%)" ] ; then - echo "<tr><td>$name</td><td>${unz}%</td></tr>" >> $output + echo "<tr><td>$name</td><td>${allz}%</td></tr>" >> $output else - echo "<tr><td>$name</td><td>${unx}/${uny} (${unz}%)</td></tr>" >> $output + echo "<tr><td>$name</td><td>${allx}/${ally} (${allz}%)</td></tr>" >> $output fi done < $outdir/data_${func}.txt |