Mercurial > repos > iuc > raceid_clustering
diff scripts/cluster.R @ 2:528a43b1cbcf draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/raceid3 commit 1d6e79ba92ce98c7c91f0c4076c9ca5e4e3f3a20
| author | iuc |
|---|---|
| date | Thu, 28 Feb 2019 17:40:05 -0500 |
| parents | 89ee61bcc310 |
| children | d4646ce659b4 |
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--- a/scripts/cluster.R Thu Feb 28 12:59:53 2019 -0500 +++ b/scripts/cluster.R Thu Feb 28 17:40:05 2019 -0500 @@ -24,9 +24,9 @@ ## Get histogram metrics for library size and number of features raw.lib <- log10(colSums(as.matrix(sc@expdata))) - raw.feat <- log10(rowSums(as.matrix(sc@expdata)>0)) + raw.feat <- log10(colSums(as.matrix(sc@expdata)>0)) filt.lib <- log10(colSums(getfdata(sc))) - filt.feat <- log10(rowSums(getfdata(sc)>0)) + filt.feat <- log10(colSums(getfdata(sc)>0)) br <- 50 ## Determine limits on plots based on the unfiltered data @@ -47,18 +47,18 @@ ## feat.x_lim <- c(0,betterrange(max(tmp.feat$breaks))) par(mfrow=c(2,2)) - print(hist(raw.lib, breaks=br, main="RawData Log10(LibSize)")) # , xlim=lib.x_lim, ylim=lib.y_lim) - print(hist(raw.feat, breaks=br, main="RawData Log10(NumFeat)")) #, xlim=feat.x_lim, ylim=feat.y_lim) - print(hist(filt.lib, breaks=br, main="FiltData Log10(LibSize)")) # , xlim=lib.x_lim, ylim=lib.y_lim) - tmp <- hist(filt.feat, breaks=br, main="FiltData Log10(NumFeat)") # , xlim=feat.x_lim, ylim=feat.y_lim) - print(tmp) # required, for extracting midpoint + print(hist(raw.lib, breaks=br, main="RawData Log10 LibSize")) # , xlim=lib.x_lim, ylim=lib.y_lim) + print(hist(raw.feat, breaks=br, main="RawData Log10 NumFeat")) #, xlim=feat.x_lim, ylim=feat.y_lim) + print(hist(filt.lib, breaks=br, main="FiltData Log10 LibSize")) # , xlim=lib.x_lim, ylim=lib.y_lim) + tmp <- hist(filt.feat, breaks=br, main="FiltData Log10 NumFeat") # , xlim=feat.x_lim, ylim=feat.y_lim) + print(tmp) + ## required, for extracting midpoint unq <- unique(filt.feat) if (length(unq) == 1){ - text(tmp$mids, table(filt.feat)[[1]] - 100, pos=1, paste(format(10^unq, scientific=T, digits=3), - " Features in all Cells", sep=""), cex=0.8) + abline(v=unq, col="red", lw=2) + text(tmp$mids, table(filt.feat)[[1]] - 100, pos=1, paste(10^unq, "\nFeatures\nin remaining\nCells", sep=""), cex=0.8) } - if (filt.use.ccorrect){ par(mfrow=c(2,2)) sc <- do.call(CCcorrect, c(sc, filt.ccc))