Workflow for non-targeted LC-MS metabolic profiling
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Documentation for package ‘notameViz’ version 1.0.0
Help Pages
| manhattan_plot | Manhattan plot |
| mz_rt_plot | Plot m/z vs retention time plot (cloud plot) |
| plot_dendrogram | Sample dendrogram |
| plot_dist_density | Plot distance density |
| plot_effect_heatmap | Heatmap of effects between variables, such as correlations |
| plot_injection_lm | Estimate the magnitude of drift |
| plot_pca | PCA scatter plot |
| plot_pca_arrows | PCA plot with arrows |
| plot_pca_hexbin | PCA hexbin plot |
| plot_pca_loadings | PCA loadings plot |
| plot_p_histogram | Histogram of p-values |
| plot_quality | Plot quality metrics |
| plot_sample_boxplots | Plot a boxplot for each sample |
| plot_sample_heatmap | Sample heatmap |
| plot_tsne | t-SNE scatter plot |
| plot_tsne_arrows | t-SNE plot with arrows |
| plot_tsne_hexbin | t-SNE hexbin plot |
| save_batch_plots | Save batch correction plots |
| save_beeswarm_plots | Save beeswarm plots of each feature by group |
| save_dc_plots | Save drift correction plots |
| save_group_boxplots | Save box plots of each feature by group |
| save_group_lineplots | Save line plots with errorbars by group |
| save_plot | Save plot to chosen format |
| save_QC_plots | Write all relevant pretreatment visualizations to pdf |
| save_scatter_plots | Save scatter plots of each feature against a set variable |
| save_subject_line_plots | Save line plots with mean |
| visualize_clusters | Visualize clusters of features |
| volcano_plot | Volcano plot |