Make_AnnTable | R Documentation |
Make_AnnTable, Make a big dataframe, each row is a cell, each column includes info such as clonal UMAP, Clonal ID, ATAC/RNA/WNN UMAP, PCA, gene expression of chosen gene, etc. Require a redeemR object and a multiome wrapper that better matches the cells in the redeemR
Make_AnnTable(
redeemR = DN4_HSC_redeemR.Sensitive,
Multiome = Donor04_HSC_Multiome_wrapper,
clonal_features = c("nCount_mitoV", "seurat_clusters"),
clonal_features_rename = c("nCount_mitoV", "clone_clusters"),
CellMeta_features = c("meanCov", "nCount_RNA", "nFeature_RNA", "nCount_ATAC",
"nFeature_ATAC", "CellType"),
CellMeta_features_rename = c("Mito_meanCov", "nCount_RNA", "nFeature_RNA",
"nCount_ATAC", "nFeature_ATAC", "CellType"),
multiome_features = c("seurat_clusters"),
multiome_features_rename = c("NewSeurat_cluster"),
RNAUMAP = T,
ATACUMAP = T,
WNNUMAP = T,
PCA = F,
LSI = F,
Variants = "",
genes = "",
peaks = "",
PostTrans_from = c(2, 3),
PostTrans_to = c(2, 1)
)
redeemR |
eg. DN4_HSC_redeemR.Sensitive |
Multiome |
eg. Donor04_HSC_Multiome_wrapper, Multiome_wrapper object that matches with the redeemR, a reclustering using Multi_Wrapper() is recommended |
clonal_features |
eg. c("nCount_mitoV","seurat_clusters"), The column names take from redeemR@Seurat@meta.data, importantly the clonal clusterings |
clonal_features_rename |
eg. c("nCount_mitoV","clone_clusters") Rename the clonal_features |
CellMeta_features |
eg. c("meanCov","nCount_RNA","nFeature_RNA","nCount_ATAC","nFeature_ATAC","CellType") The column names take from redeemR@CellMeta, may useful cell features |
CellMeta_features_rename |
eg. c("Mito_meanCov","nCount_RNA","nFeature_RNA","nCount_ATAC","nFeature_ATAC","CellType") Rename the CellMeta |
multiome_features |
eg. c("seurat_clusters") The column names take from Multiome@meta.data |
multiome_features_rename |
eg. c("NewSeurat_cluster") Rename the column names for multiome_features |
RNAUMAP |
default T |
ATACUMAP |
Default T |
WNNUMAP |
Default T |
PCA |
Default T |
LSI |
Default T |
Variants |
Default "" can be a vector of variant names format is eg "Variants10020TC" |
genes |
Default "" can be a vector of gene names, for example c("HLF","CD34") |
peaks |
Default "" can be a vector of peaks names |
PostTrans_from |
Default c(2,3) # This is a tricky part eh nmerging files are involved, find the postfix from cellranger agg for different sample |
PostTrans_to |
Default c(2,1) |
AnnTable
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