This function fetches data from an hdf5 file. It can fetch gene expression data, metadata, and reduction data from the specified file and returns a Seurat object.
Usage
FetchH5(
DataFile,
MetaFile,
name = NULL,
features = NULL,
slot = NULL,
assay = NULL,
metanames = NULL,
reduction = NULL
)Arguments
- DataFile
The path to the hdf5 file containing the data.
- MetaFile
The path to the hdf5 file containing the metadata.
- name
The name of the dataset in the hdf5 file. If not specified, the function will attempt to find the shared group name in both files.
- features
The names of the genes or features to fetch. If specified, only these features will be fetched.
- slot
The slot for the counts in the hdf5 file. If not specified, the first slot will be used.
- assay
The name of the assay to use. If not specified, the default assay in the hdf5 file will be used.
- metanames
The names of the metadata columns to fetch.
- reduction
The name of the reduction to fetch.
Examples
if (FALSE) {
data("pancreas_sub")
pancreas_sub <- Standard_SCP(pancreas_sub)
PrepareSCExplorer(pancreas_sub, base_dir = "./SCExplorer")
srt <- FetchH5(
DataFile = "./SCExplorer/Data.hdf5",
MetaFile = "./SCExplorer/Meta.hdf5",
features = c("Ins1", "Ghrl"),
metanames = c("SubCellType", "Phase"),
reduction = "UMAP"
)
CellDimPlot(srt, group.by = c("SubCellType", "Phase"), reduction = "UMAP")
FeatureDimPlot(srt, features = c("Ins1", "Ghrl"), reduction = "UMAP")
}