GEMLI is an R package to predict cell lineages (cells with a common ancestor) from single cell RNA datasets (or any other type of single-cell gene expression data) and to call genes with a high gene expression memory on the predicted cell lineages. It is described in A.S. Eisele*, M. Tarbier*, A.A. Dormann, V. Pelechano, D.M. Suter | "Barcode-free prediction of cell lineages from scRNA-seq datasets" | 2022 bioRxiv: https://www.biorxiv.org/content/10.1101/2022.09.20.508646v1
The approach is based on findings of Phillips et al. 2019 (doi.org/10.1038/s41467-019-09189-8) where it was shown that some genes show varying gene expression across cell lineages that is stable over multiple cell generation.
Simply tun: install_github("UPSUTER/GEMLI", subdir="GEMLI_package_v0"). GEMLI is now isntalled and can be used via library(GEMLI).
We are still working to make GEMLI more intuitive, user-friendly, faster and versatile. Therefore exiting functions will still be updated and new functionalities will be added. We'll publish a list of changes for each version for you to keep track. Your feedback is very welcome and will help us make GEMLI even better. What do you like about GEMLI? Something not working? What functions are you missing? Let us know! Contact: marcel.tarbier@scilifelab.se or almut.eisele@epfl.ch
First we load the example data.
> load('GEMLI_example_data_matrix.RData')
> load('GEMLI_example_barcode_information.RData')
GEMLI's inputs and outputs are stored in a list of objects with predefined names. To run GEMLI you need at least a quality controlled and normalized gene expression matrix (rows = genes/features, colums = cells/samples). In this example we also provide a ground truth for lineages stemming from a barcoding experiment (values = barcode ID, names = cell IDs).
> GEMLI_items = list()
> GEMLI_items[['gene_expression']] = data_matrix
> GEMLI_items[['barcodes']] = lineage_dict_bc
>
> GEMLI_items[['gene_expression']][9:14,1:5]
AAACGAACAGGTGTGA-1 AAAGGTAGTTGCTTGA-1 AACCACAAGTTTGTCG-1 AAGCCATGTTCCACGG-1 AAGCGAGGTACGGCAA-1
ENSMUSG00000033845 14.761746 12.9570026 13.240645 8.8596794 12.791617
ENSMUSG00000025903 3.163231 1.2340002 4.878132 0.7383066 0.000000
ENSMUSG00000033813 6.326463 5.5530011 4.181256 8.8596794 5.482122
ENSMUSG00000002459 0.000000 0.0000000 0.000000 0.0000000 0.000000
ENSMUSG00000085623 0.000000 0.0000000 0.000000 0.0000000 0.000000
ENSMUSG00000033793 3.163231 0.6170001 1.393752 2.2149199 5.482122
>
> GEMLI_items[['barcodes']][1:5]
CACAGATAGTGATGGC-1 TATCTTGGTACGGGAT-1 AAACGAACAGGTGTGA-1 AGAGAATAGGTCATAA-1 GAGTGAGTCCAGTACA-1
2 2 2 7 7
We can then identify cell lineages through repeated iterative clustering (this may take 2-3min). The predict_lineages function takes our GEMLI_items as input. It outputs a matrix of all cells against all cells with values corresponding to a confidence score that they are part of the same lineage.
> lineage_predictions_matrix = predict_lineages(GEMLI_items)
>
> lineage_predictions_matrix[1:5,15:19]
AGAGAATAGGTCATAA-1 AGAGCAGCAAGTGATA-1 AGATGCTTCAAAGACA-1 AGGATCTGTATCGTTG-1 AGGGAGTAGACGATAT-1
AAACGAACAGGTGTGA-1 0 0 0 0 14
AAAGGTAGTTGCTTGA-1 87 0 0 0 0
AACCACAAGTTTGTCG-1 0 0 0 0 39
AAGCCATGTTCCACGG-1 0 0 0 0 0
AAGCGAGGTACGGCAA-1 0 0 0 0 0
Since we have barcoding data for this dataset we can test the predicted lineages against our ground truth.
The test_lineage_prediction function again takes our GEMLI_items as input. It's important that a predcition has been run first with predict_lineages. It outputs the number of true positive predictions (TP), false positive predictions (FP), as well as precision and sensitivity for various confidence intervals. The output can be visualized by setting plot_results to true/T.
> GEMLI_items = test_lineages(GEMLI_items)
>
> GEMLI_items$testing_results
TP FP precision sensitivity
0 274 24062 0.01125904 1.0000000
10 104 128 0.44827586 0.3795620
20 90 82 0.52325581 0.3284672
30 84 56 0.60000000 0.3065693
40 80 36 0.68965517 0.2919708
50 68 22 0.75555556 0.2481752
60 64 14 0.82051282 0.2335766
70 62 10 0.86111111 0.2262774
80 58 2 0.96666667 0.2116788
90 46 0 1.00000000 0.1678832
100 34 0 1.00000000 0.1240876
>
> test_lineages(GEMLI_items, plot_results=T)
We can also investigate our predictions by visualizing them as a network with the visualize_as_network function. Here we need to set a cutoff that defines which predictions we want to consider. It represents a confidence score and high values yield fewer predictions with high precision while low values yield more predcitions with lower precision.
> visualize_as_network(GEMLI_items, cutoff=90) # left image
> visualize_as_network(GEMLI_items, cutoff=50) # right image
If a ground truth e.g. from barcoding is avalable we can set ground_truth to true/T to highlight false predictions with red edges. Cells without barcode information will be displaye in white.
> visualize_as_network(GEMLI_items, cutoff=90, ground_truth=T) # left image
> visualize_as_network(GEMLI_items, cutoff=50, ground_truth=T) # right image
Now we can extract the lineage information with the prediction_to_lineage_information function. Again we need to set a cutoff that defines which predictions we want to consider. The function outputs both a lineage table and a 'dictionary', a vector that has the lineage number as values and the cell IDs as names.
> GEMLI_items = prediction_to_lineage_information(GEMLI_items, cutoff=50)
>
> GEMLI_items$predicted_lineage_table[1:5,]
cell.ID clone.ID
[1,] "AAACGAACAGGTGTGA-1" "1"
[2,] "AAAGGTAGTTGCTTGA-1" "2"
[3,] "AACCACAAGTTTGTCG-1" "3"
[4,] "AAGCCATGTTCCACGG-1" "4"
[5,] "AAGCGAGGTACGGCAA-1" "5"
>
> GEMLI_items$predicted_lineages[1:5,]
AAACGAACAGGTGTGA-1 AAAGGTAGTTGCTTGA-1 AACCACAAGTTTGTCG-1 AAGCCATGTTCCACGG-1 AAGCGAGGTACGGCAA-1
1 2 3 4 5
In some applications it may be useful to trim lineages that are too big. For instance if it is known that cells should have undergone only a certain number of divisions effectively limiting the lineage size or if you are only interested in sister cell pairs. Similarly, if you investigate large lineages you want to avoid lineages being merged due to few false predictions between otherwise well-interconnected lineages. The suggest_network_trimming_to_size function allows you to preview what a trimming to size would look like. It will again show the predicted lineages as networks but highlight all connections that would be trimmed given a certain size restriction (max_size). If you are happy with the suggested trimming you create new trimmed GEMLI_items list, in this example we called it GEMLI_items_post_processed. You can then again visualize the predictions to see how the changes have affected your predictions.
> suggest_network_trimming_to_size(GEMLI_items, max_size=2, cutoff=50) # left image
> GEMLI_items_post_processed = trim_network_to_size(GEMLI_items, max_size=2, cutoff=50)
> visualize_as_network(GEMLI_items_post_processed, cutoff=50) # right image
If you use the package, please cite A.S. Eisele*, M. Tarbier*, A.A. Dormann, V. Pelechano, D.M. Suter | "Barcode-free prediction of cell lineages from scRNA-seq datasets" | 2022 bioRxiv: https://www.biorxiv.org/content/10.1101/2022.09.20.508646v1