From f96a5d4d134b225b6b0ff414363c955bd4b56c1e Mon Sep 17 00:00:00 2001 From: jonathan-columbiau Date: Thu, 8 Feb 2024 22:48:15 -0500 Subject: [PATCH] trying to get this to work --- DESCRIPTION | 4 ++-- README.md | 2 ++ man/AlignBPCellsObjs.Rd | 2 +- man/test_ex_data_bpcells.Rd | 23 +++++++++++++++++++++++ man/test_ex_metadata.Rd | 23 +++++++++++++++++++++++ man/train_ex_data_bpcells.Rd | 23 +++++++++++++++++++++++ man/train_ex_metadata.Rd | 23 +++++++++++++++++++++++ vignettes/Basic-Tutorial.Rmd | 9 +++++++-- 8 files changed, 104 insertions(+), 5 deletions(-) create mode 100644 man/test_ex_data_bpcells.Rd create mode 100644 man/test_ex_metadata.Rd create mode 100644 man/train_ex_data_bpcells.Rd create mode 100644 man/train_ex_metadata.Rd diff --git a/DESCRIPTION b/DESCRIPTION index f96a274..de20c15 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -26,7 +26,6 @@ Depends: ranger, Seurat, SeuratObject, - SeuratData, stats, stringr, testthat, @@ -34,7 +33,8 @@ Depends: tidyr, R (>= 2.10) Remotes: - bnprks/BPCells + bnprks/BPCells, + satijalab/seurat-data URL: https://github.com/jonathan-columbiau/lionmap, https://jonathan-columbiau.github.io/lionmap/ BugReports: https://github.com/jonathan-columbiau/lionmap/issues Suggests: diff --git a/README.md b/README.md index 9f278ff..877dfc0 100644 --- a/README.md +++ b/README.md @@ -4,6 +4,8 @@ This package is meant to enable easy, consistent and robust cell type mapping us There are a few different packages you have to install to use this package that are not hosted on the CRAN package directory. For most users, that will mean you have to manually install them (click the links below for instructions to install the following packages). You should also install the remotes library to install this package from Github. +Steps to have a successful install: + 1) Install the BPCells package (for more information [see here](https://bnprks.github.io/BPCells/)) 2) Install the [treeio package](https://bioconductor.org/packages/release/bioc/html/treeio.html) diff --git a/man/AlignBPCellsObjs.Rd b/man/AlignBPCellsObjs.Rd index 7803437..2682927 100644 --- a/man/AlignBPCellsObjs.Rd +++ b/man/AlignBPCellsObjs.Rd @@ -21,6 +21,6 @@ query datasets in the proper format before finding marker genes). } \examples{ -bpcells_obj1 = AlignBPCellsObjs(bpcells_obj1, bpcells_obj2) +train_ex_data_bpc = AlignBPCellsObjs(bpcells_obj1, bpcells_obj2) bpcells_obj2 = AlignBPCellsObjs(bpcells_obj2, bpcells_obj1) } diff --git a/man/test_ex_data_bpcells.Rd b/man/test_ex_data_bpcells.Rd new file mode 100644 index 0000000..1c630d6 --- /dev/null +++ b/man/test_ex_data_bpcells.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{test_ex_data_bpcells} +\alias{test_ex_data_bpcells} +\title{PBMC 3k dataset subset} +\format{ +\subsection{\code{test_ex_data_bpcells}}{ + +A bpcells object +} +} +\source{ +\url{https://www.10xgenomics.com/datasets/3-k-pbm-cs-from-a-healthy-donor-1-standard-1-1-0} +} +\usage{ +test_ex_data_bpcells +} +\description{ +A subset of pbmc3k data stored in BPCells format used as test data in +vignette and examples. +} +\keyword{datasets} diff --git a/man/test_ex_metadata.Rd b/man/test_ex_metadata.Rd new file mode 100644 index 0000000..41fe9d0 --- /dev/null +++ b/man/test_ex_metadata.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{test_ex_metadata} +\alias{test_ex_metadata} +\title{PBMC 3k dataset testing metadata} +\format{ +\subsection{\code{test_ex_metadata}}{ + +A bpcells object +} +} +\source{ +\url{https://github.com/satijalab/seurat-data} +} +\usage{ +test_ex_metadata +} +\description{ +Metadata of pbmc3k dataset subset using Seurat annotations, taken from Seurat data +package. +} +\keyword{datasets} diff --git a/man/train_ex_data_bpcells.Rd b/man/train_ex_data_bpcells.Rd new file mode 100644 index 0000000..37844c5 --- /dev/null +++ b/man/train_ex_data_bpcells.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{train_ex_data_bpcells} +\alias{train_ex_data_bpcells} +\title{PBMC 3k dataset subset} +\format{ +\subsection{\code{train_ex_data_bpcells}}{ + +A bpcells object +} +} +\source{ +\url{https://www.10xgenomics.com/datasets/3-k-pbm-cs-from-a-healthy-donor-1-standard-1-1-0} +} +\usage{ +train_ex_data_bpcells +} +\description{ +A subset of pbmc3k data stored in BPCells format used as training data in +vignette and examples. +} +\keyword{datasets} diff --git a/man/train_ex_metadata.Rd b/man/train_ex_metadata.Rd new file mode 100644 index 0000000..ebd833e --- /dev/null +++ b/man/train_ex_metadata.Rd @@ -0,0 +1,23 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/data.R +\docType{data} +\name{train_ex_metadata} +\alias{train_ex_metadata} +\title{PBMC 3k dataset training metadata} +\format{ +\subsection{\code{train_ex_metadata}}{ + +A bpcells object +} +} +\source{ +\url{https://github.com/satijalab/seurat-data} +} +\usage{ +train_ex_metadata +} +\description{ +Metadata of pbmc3k dataset subset using Seurat annotations, taken from Seurat data +package. +} +\keyword{datasets} diff --git a/vignettes/Basic-Tutorial.Rmd b/vignettes/Basic-Tutorial.Rmd index fa85869..a8cab09 100644 --- a/vignettes/Basic-Tutorial.Rmd +++ b/vignettes/Basic-Tutorial.Rmd @@ -24,8 +24,13 @@ issues accessing the data needed for this tutorial. ```{r} library(lionmap) -InstallData("pbmc3k") -UpdateSeuratObject(pbmc3k) #just Seurat updating things to get it to work +library(SeuratData) +library(Seurat) +library(BPCells) +library(magrittr) +library(caret) +SeuratData::InstallData("pbmc3k") +SeuratObject::UpdateSeuratObject(pbmc3k) #just Seurat updating things to get it to work ``` 1. Get gene expression data in a BPCells matrix and cell type