v0.0.3

Author: ggirelli

CHANGELOG.md

@@ -8,6 +8,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ###  ...
 - ...
 
+## [0.0.3] - 2019-08-02
+### Fixed
+- Bug that converted NA's to 0s.
+
 ## [0.0.2] - 2019-06-20
 ### Added
 - Options for choosing which legend(s) to show.
@@ -23,3 +27,5 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 [Unreleased] https://github.com/ggirelli/ggkaryo/
 [0.0.1] https://github.com/ggirelli/gpseq-img-py/releases/tag/v0.0.1
+[0.0.2] https://github.com/ggirelli/gpseq-img-py/releases/tag/v0.0.2
+[0.0.3] https://github.com/ggirelli/gpseq-img-py/releases/tag/v0.0.3

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: ggkaryo2
 Title: Overlay karyotype and data-track profiles in a ggplot-compatible manner
-Version: 0.0.2
+Version: 0.0.3
 Authors@R: person("Gabriele", "Girelli", email = "gigi.ga90@gmail.com", role = c("aut", "cre"))
 Author: Gabriele Girelli [aut, cre]
 Maintainer: Gabriele Girelli <gigi.ga90@gmail.com>

R/ggkaryo.R

@@ -529,7 +529,7 @@ ggkaryo <- setRefClass("ggkaryo",
       track = track[, 1:5]
       colnames(track) = c("chrom", "start", "end", "name", "value")
       track[, chromID := unlist(lapply(chrom, .self$chrom2id))]
-      track[is.na(value), value := 0]
+      #track[is.na(value), value := 0]
 
       track = track[order(start)]
       track = track[order(chromID)]
@@ -618,7 +618,7 @@ ggkaryo <- setRefClass("ggkaryo",
 
     add_arm_boxes = function() {
       "Adds boxes around chromosome arms."
-      .self$data$plot$trackLayer = .self$data$plot$trackLayer + geom_path(
+      .self$data$plot$baseLayer = .self$data$plot$baseLayer + geom_path(
         data=.self$data[['boxes']], aes(group=paste0(chrom, "_", arm_id)),
         color="black")
     },

README.md

@@ -26,54 +26,7 @@ Usage
 
 ```R
 require(ggkaryo2)
-require(data.table)
-
-# Load example data
-data('giemsa', package='ggkaryo2')
-data('track', package='ggkaryo2')
-data('lois', package='ggkaryo2')
-
-# Plot ideogram
-ggk = ggkaryo(giemsa)
-ggk$plot_full()
-
-# Plot ideogram with boxes around chromosome arms and labels
-ggk = ggkaryo(giemsa)
-ggk$add_arm_boxes()
-ggk$add_chrom_labels()
-ggk$plot_full()
-
-# Plot ideogram with one profile track
-ggk = ggkaryo(giemsa)
-binnedTrack = track
-ggk$add_track(binnedTrack, 1e5)
-ggk$plot_full()
-
-# Plot ideogram with two profile tracks on the same side
-ggk = ggkaryo(giemsa)
-binnedTrack2 = copy(binnedTrack)
-binnedTrack2[, value := value*abs(rnorm(nrow(binnedTrack2)))]
-ggk$add_track(binnedTrack, 1e5)
-ggk$add_track(binnedTrack2, 1e5)
-ggk$plot_full()
-
-# Plot ideogram with two profile tracks on opposite sides
-ggk = ggkaryo(giemsa, opposite=T)
-binnedTrack2 = copy(binnedTrack)
-binnedTrack2[, value := value*abs(rnorm(nrow(binnedTrack2)))]
-ggk$add_track(binnedTrack, 1e5)
-ggk$add_track(binnedTrack2, 1e5)
-ggk$plot_full()
-
-# Plot ideogram with two profile tracks on opposite sides and central lois
-ggk = ggkaryo(giemsa)
-binnedTrack2 = copy(binnedTrack)
-binnedTrack2[, value := value*abs(rnorm(nrow(binnedTrack2)))]
-ggk$add_track(binnedTrack, 1e5)
-ggk$add_track(binnedTrack2, 1e5)
-loiData = lois
-ggk$add_lois(loiData, "center", "sample")
-ggk$plot_full()
+?ggkaryo
 ```
 
 Contributing