scDotPlot v0.99.0

.Rbuildignore

@@ -0,0 +1,5 @@
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.tmp\.drivedownload$
+^\.tmp\.driveupload$
+^LICENSE\.md$

.gitignore

@@ -0,0 +1,13 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+.DS_Store
+*.Rproj
+docs
+.tmp.drivedownload
+.tmp.driveupload
+inst/doc
+.Rdata
+.httr-oauth
+.quarto

DESCRIPTION

@@ -0,0 +1,61 @@
+Package: scDotPlot
+Title: Cluster a Single-cell RNA-seq Dot Plot
+Version: 0.99.0
+Authors@R: c(
+    person(given = c("Benjamin", "I"),
+           family = "Laufer",
+           role = c("aut", "cre"),
+           email = "[email protected]"),
+    person(given = c("Brad", "A"),
+           family = "Friedman",
+           role = c("aut")))
+Description: Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.
+License: Artistic-2.0
+URL: https://github.com/ben-laufer/scDotPlot
+BugReports: https://github.com/ben-laufer/scDotPlot/issues
+biocViews: 
+    Software,
+    Visualization,
+    DifferentialExpression,
+    GeneExpression,
+    Transcription,
+    RNASeq,
+    SingleCell,
+    Sequencing,
+    Clustering
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.1
+Depends:
+    R (>= 4.4.0)
+Imports: 
+    aplot,
+    BiocGenerics,
+    cli,
+    dplyr,
+    ggplot2,
+    ggsci,
+    ggtree,
+    grDevices,
+    magrittr,
+    purrr,
+    rlang,
+    scales,
+    scater,
+    Seurat,
+    SingleCellExperiment,
+    stats,
+    stringr,
+    tibble,
+    tidyr
+Suggests: 
+    AnnotationDbi,
+    knitr,
+    rmarkdown,
+    scQC,
+    scran,
+    scRNAseq,
+    scuttle,
+    SeuratObject
+VignetteBuilder: knitr
+LazyData: false

NAMESPACE

@@ -0,0 +1,42 @@
+# Generated by roxygen2: do not edit by hand
+
+S3method(scDotPlot,Seurat)
+S3method(scDotPlot,SingleCellExperiment)
+S3method(scDotPlot,default)
+export(scDotPlot)
+import(aplot)
+import(ggplot2)
+import(ggtree)
+importFrom(BiocGenerics,as.data.frame)
+importFrom(Seurat,DefaultAssay)
+importFrom(Seurat,DotPlot)
+importFrom(SingleCellExperiment,colData)
+importFrom(SingleCellExperiment,rowData)
+importFrom(cli,cli_abort)
+importFrom(dplyr,case_when)
+importFrom(dplyr,distinct)
+importFrom(dplyr,left_join)
+importFrom(dplyr,mutate)
+importFrom(dplyr,pull)
+importFrom(dplyr,rename)
+importFrom(dplyr,select)
+importFrom(ggsci,scale_fill_cosmic)
+importFrom(ggsci,scale_fill_d3)
+importFrom(grDevices,colorRampPalette)
+importFrom(magrittr,"%$%")
+importFrom(magrittr,"%>%")
+importFrom(purrr,map)
+importFrom(purrr,pluck)
+importFrom(purrr,reduce)
+importFrom(purrr,set_names)
+importFrom(rlang,sym)
+importFrom(rlang,syms)
+importFrom(scales,muted)
+importFrom(scater,plotDots)
+importFrom(stats,dist)
+importFrom(stats,hclust)
+importFrom(stringr,str_sort)
+importFrom(tibble,as_tibble)
+importFrom(tibble,column_to_rownames)
+importFrom(tibble,rownames_to_column)
+importFrom(tidyr,pivot_wider)

NEWS.md

@@ -0,0 +1,3 @@
+# scDotPlot 0.99.0
+
+* Pre-release version of the package

R/scDotPlot-package.R

@@ -0,0 +1,11 @@
+#' @keywords internal
+"_PACKAGE"
+
+utils::globalVariables(c(".", "Average", "Feature", "Group", "NumDetected",
+                         "avg.exp.scaled", "data", "features.plot",
+                         "id", "pct.exp", ":="))
+
+## usethis namespace: start
+#' @importFrom magrittr %>% %$%
+## usethis namespace: end
+NULL