quantiplot {quantiseqr} | R Documentation

## Plot the information on the tumor immune contexture

### Description

Plot the information on the tumor immune contexture, as extracted with `run_quantiseqr()`

### Usage

    quantiplot(obj)

### Arguments

`obj` | An object, either a `SummarizedExperiment` where the quantifications are stored a simple data.frame object, as obtained by `run_quantiseqr()`

### Value

A ggplot object

### Examples

    data(dataset_racle)
    dim(dataset_racle$expr_mat)
    res_quantiseq_run <- quantiseqr::run_quantiseq(
      expression_data = dataset_racle$expr_mat,
      signature_matrix = "TIL10",
      is_arraydata = FALSE,
      is_tumordata = TRUE,
      scale_mRNA = TRUE
    )

    # using a SummarizedExperiment object
    library("SummarizedExperiment")
    se_racle <- SummarizedExperiment(
      assays = List(
        abundance = dataset_racle$expr_mat
      ),
      colData = DataFrame(
        SampleName = colnames(dataset_racle$expr_mat)
      )
    )

    res_run_SE <- quantiseqr::run_quantiseq(
        expression_data = se_racle,
        signature_matrix = "TIL10",
        is_arraydata = FALSE,
        is_tumordata = TRUE,
        scale_mRNA = TRUE
    )

    quantiplot(res_quantiseq_run)
    # equivalent to...
    quantiplot(res_run_SE)

[Package quantiseqr version 1.2.0 Index]