Entering edit mode
                    2.9 years ago
        cdeantoneo31
        
    
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    20
    I am trying to analyze the data from a paper, and was presented with an mtx file, barcode.tsv, and genes.tsv. i can successfully add these into R as a seurat object, but instead of doing clustering myself I would like to use a txt file that was uploaded along with these other files, which seems to include their clustering and the coordinates for a umap
the txt is below
                      cluster   CellType    condition   HashAssignment  UMAP_1  UMAP_2
AAACCCAAGAGCAAGA-1_1    3   Fibroblast  WT  B0308   -1.40413515808334   4.42566178583769
AAACCCACATCTGCGG-1_1    1   Immune  WT  B0308   3.24737412688981    -8.88317419743868
AAACCCATCGATGCAT-1_1    0   Fibroblast  WT  B0309   -2.68064873459091   3.80931518816618
AAACGAACAACTCCAA-1_1    3   Fibroblast  WT  B0310   2.87252790687333    5.71203921579984
AAACGAACAGCTGGTC-1_1    5   Fibroblast  WT  B0306   -4.88596980812301   3.06808994555143
AAACGAATCAGCGGAA-1_1    0   Fibroblast  WT  B0307   -3.71260421516647   8.08994601511625
AAACGAATCCTGGGAC-1_1    0   Fibroblast  WT  B0307   -3.86652391197433   7.87874720835355
However, I cannot figure out how to do this. It seems like the best way would be to add the information to the mtx meta. Am I on the right track, and if so how would I go about doing this?
The only thing I can think of is to add the cluster
You can use
obj@meta.datato reference the metadata data frame directly, soobj@meta.data$myclust <- read.csv('myclust.csv')$clustermay do the trick -- so long as the file has exactly the same number of cells in exactly the same order as the barcode.tsv file.