quantiplot {quantiseqr} | R Documentation |
Plot the information on the tumor immune contexture, as extracted with
run_quantiseqr()
quantiplot(obj)
obj |
An object, either
|
A ggplot object
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)