Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 47:099cc1254f74 draft

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author davidvanzessen
date Mon, 09 Nov 2015 07:21:09 -0500
parents 9afd8430de2c
children 5c6b9e99d576
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46:42e39033514b 47:099cc1254f74
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358 dat$percentage_mutations = round(dat$VRegionMutations / dat$VRegionNucleotides * 100, 2) 358 dat$percentage_mutations = round(dat$VRegionMutations / dat$VRegionNucleotides * 100, 2)
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360 p = ggplot(dat, aes(best_match, percentage_mutations)) 360 p = ggplot(dat, aes(best_match, percentage_mutations))
361 p = p + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA) + geom_point(aes(colour=best_match), position="jitter") 361 p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA)
362 p = p + xlab("Subclass") + ylab("Frequency") + ggtitle("Frequency scatter plot") 362 p = p + xlab("Subclass") + ylab("Frequency") + ggtitle("Frequency scatter plot")
363 write.table(dat[,c("Sequence.ID", "best_match", "VRegionMutations", "VRegionNucleotides", "percentage_mutations")], "scatter.txt", sep="\t",quote=F,row.names=F,col.names=T) 363 write.table(dat[,c("Sequence.ID", "best_match", "VRegionMutations", "VRegionNucleotides", "percentage_mutations")], "scatter.txt", sep="\t",quote=F,row.names=F,col.names=T)
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366 png(filename="scatter.png") 366 png(filename="scatter.png")