permutation_test_plot {AlpsNMR} | R Documentation |
Plot permutation test using actual model and permutated models
permutation_test_plot( nmr_data_analysis_model, permMatrix, xlab = "AUCs", xlim, ylim = NULL, breaks = "Sturges", main = "Permutation test" )
nmr_data_analysis_model |
A nmr_data_analysis_model |
permMatrix |
A permutation fitness outcome from permutation_test_model |
xlab |
optional xlabel |
xlim |
optional x-range |
ylim |
otional y-range |
breaks |
optional custom histogram breaks (defaults to 'sturges') |
main |
optional plot title (or TRUE for autoname) |
A plot with the comparison between the actual model versus the permuted models
# Data analysis for a table of integrated peaks ## Generate an artificial nmr_dataset_peak_table: ### Generate artificial metadata: num_samples <- 32 # use an even number in this example num_peaks <- 20 metadata <- data.frame( NMRExperiment = as.character(1:num_samples), Condition = rep(c("A", "B"), times = num_samples/2), stringsAsFactors = FALSE ) ### The matrix with peaks peak_means <- runif(n = num_peaks, min = 300, max = 600) peak_sd <- runif(n = num_peaks, min = 30, max = 60) peak_matrix <- mapply(function(mu, sd) rnorm(num_samples, mu, sd), mu = peak_means, sd = peak_sd) colnames(peak_matrix) <- paste0("Peak", 1:num_peaks) ## Artificial differences depending on the condition: peak_matrix[metadata$Condition == "A", "Peak2"] <- peak_matrix[metadata$Condition == "A", "Peak2"] + 70 peak_matrix[metadata$Condition == "A", "Peak6"] <- peak_matrix[metadata$Condition == "A", "Peak6"] - 60 ### The nmr_dataset_peak_table peak_table <- new_nmr_dataset_peak_table( peak_table = peak_matrix, metadata = list(external = metadata) ) methodology <- plsda_auroc_vip_method(ncomp = 3) model <- nmr_data_analysis( peak_table, y_column = "Condition", identity_column = NULL, external_val = list(iterations = 3, test_size = 0.25), internal_val = list(iterations = 3, test_size = 0.25), data_analysis_method = methodology ) p = permutation_test_model(peak_table, y_column = "Condition", identity_column = NULL, external_val = list(iterations = 3, test_size = 0.25), internal_val = list(iterations = 3, test_size = 0.25), data_analysis_method = methodology, nPerm = 10) permutation_test_plot(model, p)