diff --git a/DESCRIPTION b/DESCRIPTION index 0e9e3e64..aa4ca380 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: scRepertoire Title: A toolkit for single-cell immune receptor profiling -Version: 2.0.5 +Version: 2.0.6 Authors@R: c( person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"), person(given = "Qile", family = "Yang", role = c("aut"), email = "qile.yang@berkeley.edu"), diff --git a/NEWS.md b/NEWS.md index d26d4443..d1c32817 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,8 @@ +# scRepertoire VERSION 2.0.6 + +## UNDERLYING CHANGES +* Fixed issue with custom column headers for clones + # scRepertoire VERSION 2.0.5 ## UNDERLYING CHANGES diff --git a/R/utils.R b/R/utils.R index 9adaa929..a6a86185 100644 --- a/R/utils.R +++ b/R/utils.R @@ -360,12 +360,9 @@ "ctstrict" = "CTstrict" ) - x <- tolower(x) - - if (!is.null(clonecall_dictionary[[x]])) { - return(clonecall_dictionary[[x]]) - } - else { + if (!is.null(clonecall_dictionary[[tolower(x)]])) { + return(clonecall_dictionary[[tolower(x)]]) + } else { warning("A custom variable ", x, " will be used to call clones") return(x) } diff --git a/tests/testthat/_snaps/StartractDiversity/startracdiversity-plot.new.svg b/tests/testthat/_snaps/StartractDiversity/startracdiversity-plot.new.svg new file mode 100644 index 00000000..af181bdd --- /dev/null +++ b/tests/testthat/_snaps/StartractDiversity/startracdiversity-plot.new.svg @@ -0,0 +1,344 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +migr + + + + + + + + + + +tran + + + + + + + + + + +expa + + + + + + + + + + + + + + + + + + + + +1 +2 +3 +4 +5 +6 +7 +8 +9 +10 +11 +12 +13 +14 +15 +16 +17 + +0.0 +0.1 +0.2 +0.3 + + + + + +0.0 +0.1 +0.2 +0.3 + + + + + +0.0 +0.1 +0.2 +0.3 + + + + +Index Score +StartracDiversity_plot + + diff --git a/tests/testthat/_snaps/clonalOverlay/clonaloverlay-clonalproportion-plot.new.svg b/tests/testthat/_snaps/clonalOverlay/clonaloverlay-clonalproportion-plot.new.svg new file mode 100644 index 00000000..530df22f --- /dev/null +++ b/tests/testthat/_snaps/clonalOverlay/clonaloverlay-clonalproportion-plot.new.svg @@ -0,0 +1,654 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +P19 + + + + + + + + + + +P20 + + + + + + + + + + +P17 + + + + + + + + + + +P18 + + + + + + + +-4 +0 +4 +8 + + + + + +-4 +0 +4 +8 + +-5 +0 +5 + + + + +-5 +0 +5 + + + +Dimension 1 +Dimension 2 +clonalOverlay_clonalProportion_plot + + diff --git a/tests/testthat/_snaps/clonalOverlay/clonaloverlay-plot.new.svg b/tests/testthat/_snaps/clonalOverlay/clonaloverlay-plot.new.svg new file mode 100644 index 00000000..d44f8275 --- /dev/null +++ b/tests/testthat/_snaps/clonalOverlay/clonaloverlay-plot.new.svg @@ -0,0 +1,681 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +P19 + + + + + + + + + + +P20 + + + + + + + + + + +P17 + + + + + + + + + + +P18 + + + + + + + +-4 +0 +4 +8 + + + + + +-4 +0 +4 +8 + +-5 +0 +5 + + + + +-5 +0 +5 + + + +Dimension 1 +Dimension 2 +clonalOverlay_plot + + diff --git a/tests/testthat/_snaps/clonalRarefaction/clonalclonalrarefaction-h2-p3-plot.new.svg b/tests/testthat/_snaps/clonalRarefaction/clonalclonalrarefaction-h2-p3-plot.new.svg new file mode 100644 index 00000000..33091eda --- /dev/null +++ b/tests/testthat/_snaps/clonalRarefaction/clonalclonalrarefaction-h2-p3-plot.new.svg @@ -0,0 +1,60 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +0 +500 +1000 +1500 + + + + + + + + + +0.0 +0.2 +0.4 +0.6 +Sample coverage +Species diversity +clonalclonalRarefaction_h2_p3_plot + + diff --git a/tests/testthat/_snaps/clonalSizeDistribution/clonalsizedistribution-plot.new.svg b/tests/testthat/_snaps/clonalSizeDistribution/clonalsizedistribution-plot.new.svg new file mode 100644 index 00000000..11e5d3c7 --- /dev/null +++ b/tests/testthat/_snaps/clonalSizeDistribution/clonalsizedistribution-plot.new.svg @@ -0,0 +1,94 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +P19B +P20B +P20L +P17L +P19L +P17B +P18B +P18L + + + + + + + + + + + + + + + + + + + +-0.1 +0.0 +0.1 +0.2 +0.3 +0.4 +0.5 +clonalSizeDistribution_plot + +