reportceldaCG {celda} | R Documentation

## Generate an HTML report for celda_CG

### Description

`reportCeldaCGRun` will run recursiveSplitModule and recursiveSplitCell to find the number of modules (`L`) and the number of cell populations (`K`). A final celda_CG model will be selected from recursiveSplitCell. After a celda_CG model has been fit, `reportCeldaCGPlotResults` can be used to create an HTML report for visualization and exploration of the celda_CG model results. Some of the plotting and feature selection functions require the installation of the Bioconductor package `singleCellTK`.

### Usage

    reportCeldaCGRun(
      sce,
      L,
      K,
      sampleLabel = NULL,
      altExpName = "featureSubset",
      useAssay = "counts",
      initialL = 10,
      maxL = 150,
      initialK = 5,
      maxK = 50,
      minCell = 3,
      minCount = 3,
      maxFeatures = 5000,
      output_file = "CeldaCG_RunReport",
      output_sce_prefix = "celda_cg",
      output_dir = ".",
      pdf = FALSE,
      showSession = TRUE
    )

    reportCeldaCGPlotResults(
      sce,
      reducedDimName,
      features = NULL,
      displayName = NULL,
      altExpName = "featureSubset",
      useAssay = "counts",
      cellAnnot = NULL,
      cellAnnotLabel = NULL,
      exactMatch = TRUE,
      moduleFilePrefix = "module_features",
      output_file = "CeldaCG_ResultReport",
      output_dir = ".",
      pdf = FALSE,
      showSetup = TRUE,
      showSession = TRUE
    )

### Arguments

`sce` | A SingleCellExperiment with the matrix located in the assay slot under `useAssay`. Rows represent features and columns represent cells.
`L` | Integer. Final number of feature modules. See `celda_CG` for more information.
`K` | Integer. Final number of cell populations. See `celda_CG` for more information.
`sampleLabel` | Vector or factor. Denotes the sample label for each cell (column) in the count matrix.
`altExpName` | The name for the altExp slot to use. Default `"featureSubset"`.
`useAssay` | A string specifying which assay slot to use. Default `"counts"`.
`initialL` | Integer. Minimum number of modules to try. See recursiveSplitModule for more information. Defailt `10`.
`maxL` | Integer. Maximum number of modules to try. See recursiveSplitModule for more information. Default `150`.
`initialK` | Integer. Initial number of cell populations to try.
`maxK` | Integer. Maximum number of cell populations to try.
`minCell` | Integer. Minimum number of cells required for feature selection. See selectFeatures for more information. Default `3`.
`minCount` | Integer. Minimum number of counts required for feature selection. See selectFeatures for more information. Default `3`.
`maxFeatures` | Integer. Maximum number of features to include. If the number of features after filtering for `minCell` and `minCount` are greater than `maxFeature`, then Seurat's VST function is used to select the top variable features. Default `5000`.
`output_file` | Character. Prefix of the html file. Default `"CeldaCG_ResultReport"`.
`output_sce_prefix` | Character. The `sce` object with `celda_CG` results will be saved to an `.rds` file starting with this prefix. Default `celda_cg`.
`output_dir` | Character. Path to save the html file. Default `.`.
`pdf` | Boolean. Whether to create PDF versions of each plot in addition to PNGs. Default `FALSE`.
`showSession` | Boolean. Whether to show the session information at the end. Default `TRUE`.
`reducedDimName` | Character. Name of the reduced dimensional object to be used in 2-D scatter plots throughout the report. Default `celda_UMAP`.
`features` | Character vector. Expression of these features will be displayed on a reduced dimensional plot defined by `reducedDimName`. If `NULL`, then no plotting of features on a reduced dimensinoal plot will be performed. Default `NULL`.
`displayName` | Character. The name to use for display in scatter plots and heatmaps. If `NULL`, then the rownames of the `sce` object will be used. This can also be set to the name of a column in the row data of `sce` or `altExp(sce, altExpName)`. Default `NULL`.
`cellAnnot` | Character vector. The cell-level annotations to display on the reduced dimensional plot. These variables should be present in the column data of the `sce` object. Default `NULL`.
`cellAnnotLabel` | Character vector. Additional cell-level annotations to display on the reduced dimensional plot. Variables will be treated as categorial and labels for each group will be placed on the plot. These variables should be present in the column data of the `sce` object. Default `NULL`.
`exactMatch` | Boolean. Whether to only identify exact matches or to identify partial matches using `grep`. Default `FALSE`.
`moduleFilePrefix` | Character. The features in each module will be written to a a csv file starting with this name. If `NULL`, then no file will be written. Default `"module_features"`.
`showSetup` | Boolean. Whether to show the setup code at the beginning. Default `TRUE`.

### Value

.html file

### Examples

    data(sceCeldaCG)

    library(SingleCellExperiment)
    sceCeldaCG$sum <- colSums(counts(sceCeldaCG))
    rowData(sceCeldaCG)$rownames <- rownames(sceCeldaCG)
    sceCeldaCG <- reportCeldaCGRun(sceCeldaCG,
        initialL = 5, maxL = 20, initialK = 5,
        maxK = 20, L = 10, K = 5)
    reportCeldaCGPlotResults(sce = sceCeldaCG,
        reducedDimName = "celda_UMAP",
        features = c("Gene_1", "Gene_100"),
        displayName = "rownames",
        cellAnnot="sum")

[Package celda version 1.8.1 Index]