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'),