Merge branch 'main' into devel

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: numbat
 Title: Haplotype-Aware CNV Analysis from scRNA-Seq
 URL: https://github.com/kharchenkolab/numbat/, https://kharchenkolab.github.io/numbat/
-Version: 1.4.1
-Authors@R: c(person("Teng","Gao", email="[email protected]", role=c("cre", "aut")), person("Ruslan", "Soldatov", email="[email protected]", role="aut"), person("Hirak", "Sarkar", email="[email protected]", role="aut"), person("Evan", "Biederstedt", email="[email protected]", role="aut"), person("Peter", "Kharchenko", email = "[email protected]", role = "aut"))
+Version: 1.4.2
+Authors@R: c(person("Teng","Gao", email="[email protected]", role=c("cre", "aut")), person("Ruslan", "Soldatov", email="[email protected]", role="aut"), person("Hirak", "Sarkar", email="[email protected]", role="aut"), person("Evan", "Biederstedt", email="[email protected]", role="aut"), person("Peter", "Kharchenko", email = "[email protected]", role = "aut"))
 Description: A computational method that infers copy number variations (CNVs) in cancer scRNA-seq data and reconstructs the tumor phylogeny. 'numbat' integrates signals from gene expression, allelic ratio, and population haplotype structures to accurately infer allele-specific CNVs in single cells and reconstruct their lineage relationship. 'numbat' can be used to: 1. detect allele-specific copy number variations from single-cells; 2. differentiate tumor versus normal cells in the tumor microenvironment; 3. infer the clonal architecture and evolutionary history of profiled tumors. 'numbat' does not require tumor/normal-paired DNA or genotype data, but operates solely on the donor scRNA-data data (for example, 10x Cell Ranger output). Additional examples and documentations are available at <https://kharchenkolab.github.io/numbat/>. For details on the method please see Gao et al. Nature Biotechnology (2022) <doi:10.1038/s41587-022-01468-y>.
 License: MIT + file LICENSE
 Encoding: UTF-8
@@ -15,7 +15,7 @@ Imports:
     caTools,
     data.table,
     dendextend,
-    dplyr,
+    dplyr (>= 1.1.1),
     GenomicRanges,
     ggplot2,
     ggraph,
@@ -42,7 +42,7 @@ Imports:
     stringr,
     tibble,
     tidygraph,
-    tidyr,
+    tidyr (>= 1.3.0),
     vcfR,
     zoo
 Suggests: 

NEWS.md

@@ -1,3 +1,17 @@
+# numbat 1.4.2 - 09/18/2023
+
+* Fix pseudobulk plotting legend (#182)
+
+* Requirement for dplyr and tidyr versions (#189, #190)
+
+* Fix Numbat$plot_exp_roll (#169)
+
+* Fix CNV states reporting when `segs_loh` is provided (#183)
+
+* Fix `n_states` reporting (#178)
+
+* Improve error handling in `pileup_and_phase` (#179)
+
 # numbat 1.4.0 - 02/23/2023
 
 * Integration with hahmmr 

R/vis.R

@@ -162,7 +162,8 @@ plot_psbulk = function(
     p = p + geom_point(
             aes(shape = str_detect(state_post, '_2'), alpha = str_detect(state_post, '_2')),
             size = dot_size,
-            na.rm = TRUE
+            na.rm = TRUE,
+            show.legend = TRUE
         ) +
         geom_hline(
             data = data.frame(y = c(0,1), variable = 'pHF'),