single cell Mapper (scMappR)

Dustin Sokolowski

2021-05-14

Install and load scMappR

scMappR relies on the following dependencies which should be downloaded/updated with scMappR automatically. Please ensure that these packages are not open when installing scMappR.

Install GSVA and pcaMethods from bioconductor first, as devtools::install_githb() will automatically install CRAN.

  1. Github (Development Version)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

BiocManager::install("pcaMethods")
BiocManager::install("GSVA")

devtools::install_github("wilsonlabgroup/scMappR")
  1. CRAN (Stable Release)
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
if (!requireNamespace("devtools", quietly = TRUE))
    install.packages("devtools")

BiocManager::install("pcaMethods")
BiocManager::install("GSVA")

install.packages("scMappR")

Downloading Files.

Before using scMappR, we strongly recommend that you download data files from “https://github.com/wilsonlabgroup/scMappR_Data”.Tthe rda_path parameter will allow users to set the directory where these data are stored. If the correct files are not stored in this directory, then scMappR will download these as temporary files from “https://github.com/wilsonlabgroup/scMappR_Data”, use them in the function, and not save them. This parameter is set to "" as a default and thus data are downloaded as a default.

Additionally, the get_signature_matrices() function allows the user to get the list of all stored signature matrices at any given time. Input “all”, “pVal”, or “OR” to get the matrix of p-values, odds-ratios, or both. This function outputs the signature matrices, the top 30 cell-type markers for each cell-type, and the predicted cluster label from the Fisher’s exact test and GSVA.

signatures <- get_signature_matrices(type = "all") #return a list of cell-type labels, p-values, and odds-ratios.

Saving results.

Many of the functions in scMappR print files or generate directories. To return the full output of scMappR, please change the ‘toSave’ parameters from FALSE to TRUE in any of the functions being used. Otherwise, the functions in scMappR will only return a small portion of what scMappR has to offer. Due to CRAN packages not allowing for their packages to print files/make directories, toSave is set to FALSE as default. Furthermore, a path directory must be set. For example path="./" will print files and directories to the working directory. These measures are to prevent any file overwriting. This vignette sets path to tempdir(). When using scMappR, change tempdir() to the directories where files should be saved.

Introduction of the primary functions highlighted in the vignette.

Transforming summary statistics of differentially expressed genes by cell-type specific information

Enriching cell-type markers in a list of genes.

Processing scRNA-seq count data into a gene list.

cell-weighted Fold Changes (cwFold-changes) Generation

The scMappR_and_pathway_analysis() function generates cellWeighted_Foldchanges based on an inputted signature matrix, normalized RNA-seq count matrix (e.g. TPM, RPKM, CPM), and list of differentially-expressed genes (DEGs) before creating cell-weighted Fold Changes (cwFold-changes). cwFold-changes are row-normalized and visualized in a heatmap. Cell-type markers within calculated cwFold-changes are also visualized both as cell-type markers on their own (i.e. just their cell-type specificity), and as cwFold-changes. Then, for each cell-type, this function filters genes expressed in each cell-type (cwFold-change > 1e-5), reorders the genes by cwFold-change, then completes an ordered pathway analysis with g:ProfileR or gprofiler2 package (user chooses). All genes detected in the bulk RNA-seq are used as the background.   The example below has toSave = FALSE, up_and_downregulated = FALSE and internet = FALSE. When running scMappR yourself, it is strongly recommended to set all to TRUE. toSave = TRUE allows for the printing of folders, images, and files onto a desktop/cluster. up_and_downregulated = TRUE repeats pathway analysis for up and down-regulated genes separately. internet = TRUE allows for the completion of pathway analysis altogether. Tissue-types are available in data(scMappR_tissues), and the signature matrices themselves from get_signature_matrices(type = "OR").

Example

Output

Saved outputs

Assuming toSave = T and up_and_downregulated = T, scMappR_and_pathway_analysis() will also generate a folder in your current directory with a considerable amount of data/figures.

Here, we will walk through the output of the above example sorting by name and working downwards. * BP_barplot: a directory with pdf’s of the top 10 pathways of DEGs that have been re-normlaized by their cwFold-change. * Downregulated: a directory with pdf’s and Rdata files of pathway and TF enrichment of downregulated DEGs re-normalized by their cwFold-change. * TF_barplot: a directory with pdf’s of the top 10 TFs of DEGs that have been re-normlaized by their cwFold-change. * Upregulated: a directory with pdf’s and Rdata files of pathway and TF enrichment of upregulated DEGs re-normalized by their cwFold-change. * bulk_pathway_enrichment: png and Rdata file of traditional g:ProfilR analysis of GOBP, REAC, and KEGG databases. * bulk_TF_enrichment: png and Rdata file of traditional g:ProfilR analysis of TF database. * scMappR_vignette_cell_proportion_changes_summary: t-tests looking at difference in estimated cell-type proporitons between conditions. * scMappR_vignette_celltype_proportions: Estimated cell-type proportions of all inputted samples. * scMappR_vignette_cellWeighted_Foldchanges: cwFold-changes of all estimated DEGs. * scMappR_vignette_cwFC_downregulated_DEGs: heatmap of downregulated cwFold-changes. * scMappR_vignette_cwFC_signature_matrix_downregulated_DEGs: heatmap of downregulated cwFold-changes overlapping with signature matrix. * scMappR_vignette_DEG_signature_matrix: Heatmap of signature matrix. * scMappR_vignette_leaveOneOut_gene_proportions: estimated cell-type proportions of all samples after each DEG is removed. * scMappR_vignette_reordered_pathways: g:ProfileR enrichment of DEGs after they’re re-ordered by cwFold-changes.
* scMappR_vignette_reordered_transcription_factors: g:ProfileR enrichment of DEGs after they’re re-ordered by cwFold-changes.
* scMappR_vignette_signature_matrix: heatmap of signature matrix. * scMappR_vignette_signature_matrix_downregulated_DEGs: heatmap of signature matrix overlapping downregulated DEGs. * scMappR_vignette_signature_matrix_upregulated_DEGs: heatmap of signature matrix overlapping upregulated DEGs. * scMappR_vignetteabs_cwFC: heatmap of absolute valued cwFold-changes (up- and down-regulated DEGs). * scMappR_vignettecwFC_signature_matrix_upregulated_DEGs: heatmap of absolute valued cwFold-changes (up- and down-regulated DEGs) overlapping with the signature matrix.

Additional pathway enrichments of cwFold-changes

In addition to completing pathway enrichment of DEGs re-ranked by their cwFold-change, it may be informative to interrogate which DEGs were the most influenced by their cell-type specificity in the context of each cell-type.

Output

  • rank_increase: a list containing the rank change between DEGs and cwFold-changes. Additionally, it contains the output of g:ProfileR with genes re-ranked by eac cwFold-change.
  • non_rank_increase: the same output of pathway enrichment found in scMappR_and_pathway_analysis. Please refer to previous section for output.
Saved outputs
  • BP_barplot: Plots of the top 10 most enriched pathways by re-ranking genes by cwFold-change using g:ProfileR.
  • TF_barplot: Plots of the top 10 most enriched TFs by re-ranking genes by cwFold-change using g:ProfileR.
  • bp_reranked: Plots of the top 10 most enriched pathways by re-ordering genes based on how much the gene increases in rank between Fold-change and cwFold-change.
  • tf_reranked: Plots of the top 10 most enriched TFs by re-ordering genes based on how much the gene increases in rank between Fold-change and cwFold-change.
  • scatter_reranked: Scatter plots of the rank of cwFold-changes and regulated fold-changes of DEGs for each cell-type.
  • bulk_X_enrichment.Rdata: gProfiler results of pathway/TF enrichment of DEGs.
  • rank_increase_genes.Rdata: list showing the rank difference between Fold-changes and cwFold-changes for each cell-type.
  • reweighted_bulk_X.Rdata: List of each cell-type containing Pathway/TF enrichment of genes re-ordered by cwFold-change.
  • reweighted_reordered_X.Rdata: List of each cell-type containing Pathway/TF enrichment of genes ordered by the change in rank between fold-change and cwFold-change.

Testing the cell-type specificity of cwFold-changes at the level of the gene and cell-type.

An important aspect of scMappR is to calculate which DEGs from bulk differential analysis may be differentially expressed due to a change in expression of specific cell-types. We complete this task my measuring if the cell-type specificity of each DEG contains outliers for a specific cell-type, and if the distribution of DEGs within a cell-type (measured through cwFold-changes) is different from the distribution of DEGs measured in bulk.

Example

In this example, we are extending the output from the scMappR_and_pathway_analysis function above.

Output

Cell-type markers in a list of genes.

Given a tissue and an unranked list of genes (i.e. without a count matrix or summary statistics), the tissue_scMappR_custom() and tissue_scMappR_internal() functions visualizes cell-type markers contained within the gene-list. Then, they test for the enrichment of cell-types within that tissue. When there is no custom signature matrix, providing a tissue present in get_signature_matrices(type = "pVal") will complete cell-type specific gene visualization and enrichment for every signature matrix in the tissue.

No custom signature matrix:

Output

This function returns a list “internal”. Using the example of internal[[4]], the pre-optic area of the hypothalamus, you can see four objects.

background_heatmap
  • genesIn: genes in the signature matrix is tested.
  • genesNoIn: genes not in the signature matrix (empty).
  • geneHeat: Gene x cell-type matrix containing the cell-type rank of each gene in the signature matrix.
  • preferences: Cell-type marker genes sorted into each cell-type.
gene_list_heatmap
  • genesIn: Inputted genes that are also in the signature matrix.
  • genesNoIn: Inputted genes not in the signature matrix.
  • geneHeat: Gene x cell-type matrix containing the cell-type rank for inputted genes overlaying with genes in the signature matrix.
  • preferences: Inputted genes overlaying with signature matrix sorted into the cell-types where they’re preferentially expressed.
single_celltype_preferences
  • Output of the Fisher’s-exact test for cell-type enrichment of inputted genes with every cell-type.
group_celltype_preference
  • Identification and statistical enrichment of groups of cell-types containing the same cell-type marker genes.

Saved directory

When toSave == TRUE, a directory is generated with visualization of each signature matrix, the signature matrix subsetted by input genes, and statistical enrichment.

Custom signature matrix

tissue_scMappR_custom() assumes a custom signature matrix. We suggest a gene x cell-type matrix populated with the -log10(Padj)*sign(FC) (i.e. Rank) of the cell-type marker. We identify the cell-type marker with the FindMarker function from the Seurat package. The statistical test within that function is based on the biological question that the user interested in. Pre-computed signature matrices use the Wilcoxon test. If the value filling the matrix is not rank, users will need to change the gene_cutoff parameter to what they deem significant. If is_pvalue == TRUE, tissue_scMappR_custom() will transform the p-values into Ranks.

Output

The output is identical to that found in tissue_scMappR_internal() but with only one study, or the example shown above.

If you choose to set toSave = TRUE. This function will return a directory with a number of relevant files.

Saved Outputs

Saved directory

When toSave == TRUE, a directory is generated with visualization of each signature matrix, the signature matrix subsetted by input genes, and statistical enrichment.

Tissue by cell-type enrichment.

scMappR allows for gene-set enrichment of every cell-type marker, sorted by cell-type, tissue, and study, curated while preprocessing all of the signature matrices for the functions within scMappR. The dataset may be downloaded from https://github.com/DustinSokolowski/scMappR_Data, processed into a gmt file using a number of packages (qusage, activepathways etc.) and then used with traditional gene-set-enrichment tools (GSEA, GSVA, gprofiler). Additionally, scMappR contains the tissue_by_celltype_enrichment function, that enriches a gene list against all cell-type markers using a Fisher’s-exact test. Users can also download all cell-type markers by setting return_gmt = TRUE when using the function.

Example

Here, we will investigate the tissue x cell-type enrichment of the top 100 genes in the Preoptic area signature matrix.

Three types of outputs.

Processing scRNA-seq count data into a signature matrix.

scMappR inputs a list of count matrices (of class list, dCGMatrix, or matrix) and re-processes it using the standard Seurat V4 vignette (+ removal of cells with > 2 standard deviations of mt contamination than mean). Then, it finds cell-type markers and identifies potential cell-type names using the GSVA and Fisher’s exact methods on the CellMarker and Panglao databases. Finally, it creates a signature matrix of odds ratios and ranks. There are options to save the Seurat object, GSVA cell-type identities and list of cell-type markers. To identify what naming-preferences options described here: “brain”, “epithelial”, “endothelial”, “blood”, “connective”,“eye”, “epidermis”, “Digestive”, “Immune”, “pancreas”, “liver”, “reproductive”, “kidney”, “respiratory”

data(sm)

toProcess <- list(example = sm)

tst1 <- process_dgTMatrix_lists(toProcess, name = "testProcess", species_name = "mouse",
naming_preference = "eye", rda_path = "", 
toSave = TRUE, saveSCObject = TRUE, path = tempdir())

It is recommended to set toSave == TRUE, allowing for important data objects to be saved. Here, the above function is repeated with toSave == TRUE and saveSCObject == TRUE, and the outputted files will be briefly discussed.

Here, the following objects are saved.

Processing scRNA-seq data with multiple scRNA-seq runs.

When there are multiple scRNA-seq runs, we use the integration anchors feature to combine runs. Here, each run is a different element of the dgTMatrix_list parameter.

Making multiple run scRNA-seq data. As seen in many cases, the first dataset is identified with “.1” and the second with “.2”

Combining datasets with the integration anchors batch correction

If you do not want to use the integration anchors feature and process the scRNA-seq data as if it were one run, then keep all of these data in the same dgCMatrix matrix.

Processing scRNA-seq count data from a different species.

Please continue to use the process_from_count function. The only species specific information required in this function is the mitochondrial gene symbol to regress out mitochondria. In each of your count matrices, make sure that your michondial genes have a “MT-” preface. Then select “human” as the species. This can also be done with an “mt-” preface and selecting mouse.

Processing scRNA-seq count data when cell-types are already named.

It may be common to generate a signature matrix when clusters and cell-types have already been given for every cell. These examples follow how to make this signature matrix from:

  1. A Seurat object with named cell-types
  2. A Count matrix with named cell-types.

Signature matrix from Seurat object with named cell-type

Generating the Seurat Object for example and making up cell-types. This example will be used from 1-2.

  1. A Seurat object with named cell-types. Markers for each cell-type are stored in the generes object and each signature matrix is in gene_out.
  1. A count matrix with named cell-types.

Manually making graphics.

scMappR generates heatmaps and barplots. The barplots are generated with plotBP and make_TF_barplot. The plotting code for plotBP is provided. Inputs are a matrix called ordered_back_all of -log10(padj) and term names with the column names log10 and term_name respectively.

Barplots

Heatmaps

Here, the heatmaps are for plotting cwFold-changes and cell-type proportions. The same heatmap is used so just an example of one is given.