diff --git a/DESCRIPTION b/DESCRIPTION
index 9b5b8dd..b0af311 100644
--- a/DESCRIPTION
+++ b/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="tgaoteng@gmail.com", role=c("cre", "aut")), person("Ruslan", "Soldatov", email="soldatr@mskcc.org", role="aut"), person("Hirak", "Sarkar", email="hirak_sarkar@hms.harvard.edu", role="aut"), person("Evan", "Biederstedt", email="evan.biederstedt@gmail.com", role="aut"), person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"))
+Version: 1.4.2
+Authors@R: c(person("Teng","Gao", email="tgao@broadinstitute.org", role=c("cre", "aut")), person("Ruslan", "Soldatov", email="soldatr@mskcc.org", role="aut"), person("Hirak", "Sarkar", email="hirak_sarkar@hms.harvard.edu", role="aut"), person("Evan", "Biederstedt", email="evan.biederstedt@gmail.com", role="aut"), person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", 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 . For details on the method please see Gao et al. Nature Biotechnology (2022) .
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:
diff --git a/NEWS.md b/NEWS.md
index 541f956..8612dac 100644
--- a/NEWS.md
+++ b/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
diff --git a/R/vis.R b/R/vis.R
index 2411dbc..8376c50 100644
--- a/R/vis.R
+++ b/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'),