From 29b2b3dae38ee37cf7e83753bab72738b896c991 Mon Sep 17 00:00:00 2001 From: samuel-marsh Date: Tue, 12 Nov 2024 09:52:18 -0500 Subject: [PATCH] update docs --- NEWS.md | 1 + man/Find_Factor_Cor.Rd | 2 +- man/Read_CellBender_h5_Multi_Directory.Rd | 3 ++- 3 files changed, 4 insertions(+), 2 deletions(-) diff --git a/NEWS.md b/NEWS.md index 84e875885f..900f0d45d1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -74,6 +74,7 @@ - Added error check in `as.anndata` to explicitly check for installation of anndata before starting conversion ([#162](https://github.com/samuel-marsh/scCustomize/issues/162)). - Updated `Plot_Median_Genes`, `Plot_Median_UMIs`, `Plot_Median_Mito`, `Plot_Median_Other`, `Plot_Cells_per_Sample` to understand "ident" as grouping variable. - Updated `Store_Misc_Info_Seurat` to use Seurat accessor/setter function `Seurat::Misc()`. +- Updated documentation for `sample_names` in `Read_CellBender_h5_Multi_File` to clarify parameter behavior (related to ([#208](https://github.com/samuel-marsh/scCustomize/issues/208))). ## Fixes diff --git a/man/Find_Factor_Cor.Rd b/man/Find_Factor_Cor.Rd index e5760314c0..10004750e0 100644 --- a/man/Find_Factor_Cor.Rd +++ b/man/Find_Factor_Cor.Rd @@ -4,7 +4,7 @@ \alias{Find_Factor_Cor} \title{Find Factor Correlations} \usage{ -Find_Factor_Cor(object, reduction) +Find_Factor_Cor(object, reduction = NULL) } \arguments{ \item{object}{LIGER/Seurat object name.} diff --git a/man/Read_CellBender_h5_Multi_Directory.Rd b/man/Read_CellBender_h5_Multi_Directory.Rd index aa82d11c65..48dc56cc20 100644 --- a/man/Read_CellBender_h5_Multi_Directory.Rd +++ b/man/Read_CellBender_h5_Multi_Directory.Rd @@ -35,7 +35,8 @@ of file name that is shared across all samples. Must included the ".h5" extensi read in subdirectories in parent directory.} \item{sample_names}{a set of sample names to use for each sample entry in returned list. If \code{NULL} will -set names to the subdirectory name of each sample.} +set names to the subdirectory name of each sample. NOTE: unless \code{sample_list} is specified this will +rename files in the order they are read which will be alphabetical.} \item{h5_group_name}{Name of the group within H5 file that contains count data. This is only required if H5 file contains multiple subgroups and non-default names. Default is \code{NULL}.}