quantiplot: Plot the information on the tumor immune contexture

In federicomarini/quantiseqr: Quantification of the Tumor Immune contexture from RNA-seq data

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)

federicomarini/quantiseqr documentation built on Dec. 20, 2024, 2:39 a.m.