diff --git a/DESCRIPTION b/DESCRIPTION index 5edac3c..a7abb75 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: GENOVA Title: GENOVA: expore the Hi-C -Version: 0.8.4 +Version: 0.8.5 Authors@R: c( person("Robin H.", "van der Weide", email = "r.vd.weide@nki.nl", role = c("aut", "cre")), person("Elzo", "de Wit", email = "e.d.wit@nki.nl", role = "aut")) diff --git a/NAMESPACE b/NAMESPACE index b70faef..4f4e012 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -22,6 +22,7 @@ export(insulation.plot.dual) export(insulation.plot.single) export(insulation.score) export(intra.inter.TAD.contacts) +export(select.subset) export(stackR) export(virtual.4C) export(visualise.APA.ggplot) diff --git a/man/hic.matrixplot.Rd b/man/hic.matrixplot.Rd index 82e37d3..819d6a0 100644 --- a/man/hic.matrixplot.Rd +++ b/man/hic.matrixplot.Rd @@ -7,7 +7,9 @@ hic.matrixplot(exp1, exp2 = NULL, chrom, start, end, cut.off = 0, chip = list(NULL, NULL, NULL, NULL), bed.col = rep(c("red", "blue"), 2), bw.col = rep(c("navy", "darkred"), 2), type = rep("triangle", 4), - coplot = "dual", genes = NULL, tads = NULL, tad.type = "lower") + coplot = "dual", genes = NULL, tads = NULL, tad.type = "lower", + loops = NULL, loops.type = "lower", tads.color = "#3288bd", + loops.resize = 0, loops.color = "#3288bd") } \arguments{ \item{exp1}{The control Hi-C experiment object: produced by construct.experiment(). (bottom)} @@ -34,9 +36,17 @@ hic.matrixplot(exp1, exp2 = NULL, chrom, start, end, cut.off = 0, \item{genes}{Structure with gene information, will only be combined with bed structure} -\item{tads}{BED-like dataframe} +\item{tads}{BED-like dataframe (not a tibble or a data.table!)} \item{tad.type}{How to show TADS: upper, lower and or both} + +\item{loops}{BED-like dataframe (not a tibble or a data.table!)} + +\item{loops.type}{How to show loops: upper, lower and or both} + +\item{loops.resize}{Make the loop-boxes bigger by X bp. Can help visibility.} + +\item{loops.color}{Which color do you want the loops to have?} } \value{ A matrix-plot diff --git a/versions/GENOVA_0.8.4.tar.gz b/versions/GENOVA_0.8.5.tar.gz similarity index 58% rename from versions/GENOVA_0.8.4.tar.gz rename to versions/GENOVA_0.8.5.tar.gz index 8b97f7a..dd9efe9 100644 Binary files a/versions/GENOVA_0.8.4.tar.gz and b/versions/GENOVA_0.8.5.tar.gz differ