get_knee_df {BUSpaRse} | R Documentation

## Plot the transposed knee plot and inflection point

### Description

Plot a transposed knee plot, showing the inflection point and the number of remaining cells after inflection point filtering. It's transposed since it's more generalizable to multi-modal data.

### Usage

    get_knee_df(mat)

    get_inflection(df, lower = 100)

    knee_plot(df, inflection)

### Arguments

`mat` | Gene count matrix, a dgCMatrix.
`df` | The data frame from `get_knee_df`.
`lower` | Minimum total UMI counts for barcode for it to be considered when calculating the inflection point; this helps to avoid the noisy part of the curve for barcodes with very few counts.
`inflection` | Output of `get_inflection`.

### Value

`get_knee_df` returns a tibble with two columns: `total` for total UMI counts for each barcode, and `rank` for rank of the total counts, with number 1 for the barcode with the most counts.

`get_inflection` returns a `numeric(1)` for the total UMI count at the inflection point.

`knee_plot` returns a `ggplot2` object.

### Note

Code in part adapted from `barcodeRanks` from `DropetUtils`.

### Examples

    # Download dataset already in BUS format
    library(TENxBUSData)
    TENxBUSData(".", dataset = "hgmm100")
    tr2g <- transcript2gene(c("Homo sapiens", "Mus musculus"),
      type = "vertebrate",
      ensembl_version = 99, kallisto_out_path = "./out_hgmm100")
    m <- make_sparse_matrix("./out_hgmm100/output.sorted.txt",
      tr2g = tr2g, est_ncells = 1e5,
      est_ngenes = nrow(tr2g), TCC = FALSE)
    df <- get_knee_df(m)
    infl <- get_inflection(df)
    knee_plot(df, infl)
    # Clean up files from the example
    unlink("out_hgmm100")

[Package BUSpaRse version 1.6.1 Index]