glog_plot_optimised_lambda {pmp} | R Documentation

## Plot SSE error of lambda optimisation process

### Description

Plot SSE error of lambda optimisation process

### Usage

    glog_plot_optimised_lambda(
      df,
      optimised_lambda,
      classes,
      qc_label,
      plot_grid = 100
    )

### Arguments

`df` | A matrix-like (e.g. an ordinary matrix, a data frame) or RangedSummarizedExperiment-class object with all values of class `numeric()` or `integer()` of peak intensities, areas or other quantitative characteristic.
`optimised_lambda` | `numeric(1)`, value of optimised lambda from glog_transformation output.
`classes` | `character()`, vector of class labels. Must be the same length as the number of sample in the input peak table. If input is `SummarizedExperiment` object, use `SummarizedExperiment_object$meta_data_column_name`.
`qc_label` | `character(1)` or `NULL`, class label used to identify QC samples.
`plot_grid` | `integer(1)`, number of data points to use for SSE optimisation.

### Value

Class `ggplot` object containing optimisation plot.

### Examples

    data <- MTBLS79[, MTBLS79$Batch == 1]
    classes <- data$Class

    data <- mv_imputation(df=data, method='knn')
    out <- glog_transformation (df=data, classes=classes,
        qc_label='QC')

    optimised_lambda <- S4Vectors::metadata(out)
    optimised_lambda <-
        optimised_lambda$processing_history$glog_transformation$lambda_opt

    glog_plot_optimised_lambda(df=data, classes=classes,
        qc_label="QC", optimised_lambda=optimised_lambda)

[Package pmp version 1.2.1 Index]