Difference between revisions of "HLab:Rscripts"
From CCGB
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Scatter plots for replicates | Scatter plots for replicates | ||
*This is an example. File names and number of columns are hard coded and will need changed to match your usage. The first one plots the points all the same color. For graphs that are very dense the second one changes the colors depending on the number of bins in the vicinity of the one being plotted (red is dense). | *This is an example. File names and number of columns are hard coded and will need changed to match your usage. The first one plots the points all the same color. For graphs that are very dense the second one changes the colors depending on the number of bins in the vicinity of the one being plotted (red is dense). | ||
| − | ** [[Media:plotPairs.r.txt]] | + | ** [[Media:plotPairs.r.txt|plotPairs.r]] |
| − | ** [[Media:plotPairsDensity.r.txt]] | + | ** [[Media:plotPairsDensity.r.txt|plotPairsDensity.r]] |
PCA | PCA | ||
Revision as of 17:12, 24 October 2014
Miscellaneous R Scripts
Quantile normalization
- This can be used directly or as an example. It takes an input and output file names (tab-delimited files with header and row names). It is set up for RNA and adds 1.1 to the expression levels to avoid zeros before taking the log2(normalized expr). Media:normalize.r.txt
Scatter plots for replicates
- This is an example. File names and number of columns are hard coded and will need changed to match your usage. The first one plots the points all the same color. For graphs that are very dense the second one changes the colors depending on the number of bins in the vicinity of the one being plotted (red is dense).
PCA
GEDI
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