cosmetics

chipseq_workflow/create_igv_session.R

-#!/usr/bin/env Rscript
-
-#' # Create an IGV Session File
-#' ## Create an IGV Session File
-#' hallo
-#http://www.slideshare.net/EdwindeJonge1/docopt-user2014
-suppressMessages(library(docopt))
-
-#doc <- 'Usage: igvtrack.R --genome [options] <genome> <bam_files>...
-
-doc <- 'Usage: igvtrack.R --genome [options] <genome> <bam_files>...
-
-Options:
---cov_quantils <cov_quantils>    Use a q-value cutoff of 0.01 instead of a q-value cutoff [default: 0.8]
-'
-opts  <- docopt(doc)
-#opts <- docopt(doc, "--cov_quantils 0.7 --genome musmus test.bam naha.bam", quoted_args=T)
-
-print(opts)
-
-'
-# https://github.com/holgerbrandl/datautils/blob/master/R/spinr/spin.R
-
-export PATH=/projects/bioinfo/scripts/ngs_tools/dev/chipseq_workflow:$PATH
-create_igv_session.R  --genome  asdf lala.bam
-spin.R $(which create_igv_session.R)  \""--genome  asdf lala.bam"\"
-'
-
-require(knitr)
-require(ggplot2)
-require(dplyr)
-iris %>% head(5) %>% kable()
-
-iris %>% ggplot(aes(Sepal.Width)) + geom_histogram()
-
-
-#require(whisker)
-#bamFile="surprise.bam"
-#whisker.render("<igg file={{bamFile}}</igv>") %>% writeLines()
-#paste0("<igg file=", bamFile, "</igv>")
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