From a35dfcf7ce8c77b5aaf5cabd1304f23267f66434 Mon Sep 17 00:00:00 2001
From: Charles Plessy <charles.plessy@oist.jp>
Date: Wed, 2 Sep 2026 16:38:00 +0900
Subject: [PATCH] =?UTF-8?q?The=20inversion=20clown=E2=80=A6=20find=20it=20?=
 =?UTF-8?q?in=20your=20data.?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 R/StructuralVariants.R           |   6 ++++--
 data-raw/StructuralVariants.R    |  13 ++++++++++++-
 data/exampleClownInversion.rda   | Bin 0 -> 676 bytes
 man/StructuralVariants.Rd        |   2 ++
 vignettes/StructuralVariants.Rmd |   8 ++++++++
 5 files changed, 26 insertions(+), 3 deletions(-)
 create mode 100644 data/exampleClownInversion.rda

diff --git a/R/StructuralVariants.R b/R/StructuralVariants.R
index 1f19ada3..d7354e7f 100644
--- a/R/StructuralVariants.R
+++ b/R/StructuralVariants.R
@@ -20,11 +20,12 @@
 #' @aliases exampleDoubleInversion1 exampleDoubleInversion2
 #' @aliases exampleDoubleInversion3 exampleDoubleInversion4
 #' @aliases exampleTwinInversions exampleNotTwinInversions
-#' @aliases exampleInversionGarg2019 exampleInversionBader2001 
-#' @aliases exampleInversionHP1999fig4a exampleInversionHP1999fig4b 
+#' @aliases exampleInversionGarg2019 exampleInversionBader2001
+#' @aliases exampleInversionHP1999fig4a exampleInversionHP1999fig4b
 #' @aliases exampleInversionBergeron2005a exampleInversionBergeron2005b
 #' @aliases exampleTranslocation exampleTranslocation2
 #' @aliases exampleInsertion exampleDeletion
+#' @aliases exampleClownInversion
 #'
 #' @family Structural variants
 #'
@@ -37,6 +38,7 @@
 #' exampleInversion5uncollapsed
 #' exampleNestedInversions
 #' exampleDoubleInversion1
+#' exampleClownInversion
 #' exampleTwinInversions
 #' exampleInversionGarg2019
 #' exampleInversionBader2001
diff --git a/data-raw/StructuralVariants.R b/data-raw/StructuralVariants.R
index 2448c06f..1b20cc67 100644
--- a/data-raw/StructuralVariants.R
+++ b/data-raw/StructuralVariants.R
@@ -95,6 +95,16 @@ exampleDoubleInversion4                   <- GBreaks(exampleDoubleInversion4)
 seqlengths(exampleDoubleInversion4)       <- seqlengths(exampleDoubleInversion4$query) <- 600
 isSorted(exampleDoubleInversion4)
 
+# Clown inversion based on exampleDoubleInversion4
+# ABC/cba -> ABC/cAB -> ABC/aCB => 1-, 3+, 2+
+
+exampleClownInversion                   <- GRanges(c("chrA:100-190", "chrA:200-290", "chrA:300-340", "chrA:341-370","chrA:371-390", "chrA:400-490", "chrA:500-590"))
+strand(exampleClownInversion)           <- c(              "-",            "-",            "+",            "-",            "+",            "+",            "-"     )
+exampleClownInversion$query             <- GRanges(c("chrB:500-590", "chrB:200-290", "chrB:400-440", "chrB:441-470","chrB:471-490", "chrB:300-390", "chrB:100-190"))
+exampleClownInversion                   <- GBreaks(exampleClownInversion)
+seqlengths(exampleClownInversion)       <- seqlengths(exampleClownInversion$query) <- 600
+isSorted(exampleClownInversion)
+
 # Nested inversions
 # ABCDE -> AdcbE -> AdCbE
 
@@ -126,7 +136,7 @@ isSorted(exampleNotTwinInversions)
 
 # Example used in the paper from Garg et al. (2019).
 # {-2,5,4,-1,3,6,9,-7,-8}
-# Reversal distance = 5 reversals. 
+# Reversal distance = 5 reversals.
 # Details for Reversal distance (d) computation: 10 breakpoints (b); 5 cycles(c); 0 hurdles(h): d = b-c+h (+1 if fortress).
 exampleInversionGarg2019              <- GRanges(c("chrA:100-190", "chrA:200-290", "chrA:300-390", "chrA:400-490", "chrA:500-590", "chrA:600-690", "chrA:700-790", "chrA:800-890", "chrA:900-990"))
 strand(exampleInversionGarg2019)      <- c(              "-",            "+",            "+",            "-",            "+",            "+",            "+",            "-",            "-")
@@ -255,6 +265,7 @@ usethis::use_data(
   exampleDoubleInversion2,
   exampleDoubleInversion3,
   exampleDoubleInversion4,
+  exampleClownInversion,
   exampleNestedInversions,
   exampleTwinInversions,
   exampleNotTwinInversions,
diff --git a/data/exampleClownInversion.rda b/data/exampleClownInversion.rda
new file mode 100644
index 0000000000000000000000000000000000000000..935ef1d5174a05a24d5bb58b9a8b4f8a537ca5a4
GIT binary patch
literal 676
zcmV;V0$cq;T4*^jL0KkKSt_7z)c^!?fA0VP|KR{W3_w4pA84=d|KLCXKmY(B06+kM
z1OdPTw=n}{0Fp#Zn3^>_rqnc_q9N)YP{?|onu9<aP}9_HPc=azkkr%zPf!7%&<za$
z007COCXEbnk)}*d227YuG6q9HXbm!GU<A+@La0qp^&Ut78UO$Q8UO$Q1m8wVMH0rC
z={O2ek`hfQlmWA*0)iNZlrs^Ttac41-N{QcEdpi!FbyS)A%JF>Do4jgFUY~8)qL!n
zy*RYt1uhaA<T=QD=U7%_96QDG-!Ohg6{?10%WDgT0!6mCljh;^@3wbB0a6za8DfAV
zg*hSWoiKFO9Ru5uuR#G6UwC?<70(RbtxbHHT)K7x$&lfS3`PVvhW9NmHqdI`XO`zi
zpx9w0U}hAMgHN|KF&vPRQX&>9AOc}1s3ZU~G5l-8cN*h07Z^im-y23su0V;5ik);o
zg+%qwW<*LC6j}rcP|ysBnx_aC0VPui9ON9NL^r-n05V`HQ!tVsh=_?9h;0M`Fo+&8
z#}*#J>o}lV^w7pESFvZ<sB#QBc(diZrnifmS-{5yL9alk38t32-GZ>yR3gR(TdTXY
z9Dgh~WHBpUkWIEW&R^PQ4(&CtPAMrTfRFu6>{TGi%fk7!l`vA)Co6_}kMyxnY7OtX
z?(hW&q0T|cm>7t*)K3i(x<YqY7<kVdm-br>p4J>Pf#aI}jT{~1GEpKHIx?dQxr9YH
z%o_NlN?EUmXnP52z3?i*7^RV_lyw-hQv)H6hEHI<SDJXHhMFLk0dYt_KRIBB;-T_I
zc3P9>)k-{rCIM(+b(<wOZg;<K&Xjd%YiU*_Kzoop6|^jg9LaC=y4knrg0PtXi@744
KC`c7hH)?=xJ{yMs

literal 0
HcmV?d00001

diff --git a/man/StructuralVariants.Rd b/man/StructuralVariants.Rd
index b89f40a0..2ce9c3e9 100644
--- a/man/StructuralVariants.Rd
+++ b/man/StructuralVariants.Rd
@@ -25,6 +25,7 @@
 \alias{exampleTranslocation2}
 \alias{exampleInsertion}
 \alias{exampleDeletion}
+\alias{exampleClownInversion}
 \title{Structural Variants}
 \format{
 \code{\link{GBreaks}} objects described in more details in the
@@ -49,6 +50,7 @@ exampleInversion
 exampleInversion5uncollapsed
 exampleNestedInversions
 exampleDoubleInversion1
+exampleClownInversion
 exampleTwinInversions
 exampleInversionGarg2019
 exampleInversionBader2001
diff --git a/vignettes/StructuralVariants.Rmd b/vignettes/StructuralVariants.Rmd
index 691c2d8c..e3901130 100644
--- a/vignettes/StructuralVariants.Rmd
+++ b/vignettes/StructuralVariants.Rmd
@@ -202,6 +202,14 @@ exampleInversionBergeron2005a |> plotApairOfChrs(main = "Mathematics of Evolutio
 exampleInversionBergeron2005b |> plotApairOfChrs(main = "Mathematics of Evolution and Phylogeny (2005) - Figure 10.6")
 ```
 
+### The inversion clown.
+
+Find it in your alignments!
+
+```{r inversionClown}
+exampleClownInversion |> makeOxfordPlots(col = "strand") + ggplot2::theme_bw()
+```
+
 ## Translocations
 
 If a region has moved, but is not an inversion, then it is a translocation.