Package: notameViz 1.2.0

Vilhelm Suksi

notameViz: Workflow for non-targeted LC-MS metabolic profiling

Provides visualization functionality for untargeted LC-MS metabolomics research. Includes quality control visualizations, feature-wise visualizations and results visualizations.

Authors:Anton Klåvus [aut, cph], Jussi Paananen [aut, cph], Oskari Timonen [aut, cph], Atte Lihtamo [aut], Vilhelm Suksi [aut, cre], Retu Haikonen [aut], Leo Lahti [aut], Kati Hanhineva [aut], Ville Koistinen [ctb], Olli Kärkkäinen [ctb], Artur Sannikov [ctb]

notameViz_1.2.0.tar.gz
notameViz_1.2.0.zip(r-4.7-any)notameViz_1.2.0.zip(r-4.6-any)notameViz_1.2.0.zip(r-4.5-any)
notameViz_1.2.0.tgz(r-4.6-any)notameViz_1.2.0.tgz(r-4.5-any)
notameViz_1.2.0.tar.gz(r-4.7-any)notameViz_1.2.0.tar.gz(r-4.6-any)
notameViz_1.2.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
notameViz/json (API)

# Install 'notameViz' in R:

install.packages('notameViz', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/hanhineva-lab/notameviz/issues

On BioConductor:notameViz-1.3.0(bioc 3.24)notameViz-1.2.0(bioc 3.23)

biomedicalinformatics metabolomics dataimport massspectrometry batcheffect multiplecomparison normalization qualitycontrol visualization preprocessing

4.85 score 6 scripts 261 downloads 28 exports 73 dependencies

Last updated from:84e8961cf8 (on RELEASE_3_23). Checks:8 NOTE, 2 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	234
linux-devel	NOTE	445
source / vignettes	OK	242
linux-release	NOTE	455
macos-release	NOTE	319
macos-oldrel	NOTE	342
windows-devel	NOTE	381
windows-release	NOTE	358
windows-oldrel	NOTE	375
wasm-release	OK	131

Exports:manhattan_plot mz_rt_plot plot_dendrogram plot_dist_density plot_effect_heatmap plot_injection_lm plot_p_histogram plot_pca plot_pca_arrows plot_pca_hexbin plot_pca_loadings plot_quality plot_sample_boxplots plot_sample_heatmap plot_tsne plot_tsne_arrows plot_tsne_hexbin save_batch_plots save_beeswarm_plots save_dc_plots save_group_boxplots save_group_lineplots save_plot save_QC_plots save_scatter_plots save_subject_line_plots visualize_clusters volcano_plot

Dependencies:abind askpass beeswarm BH Biobase BiocGenerics BiocParallel cli codetools cowplot cpp11 curl DelayedArray devEMF dplyr farver formatR futile.logger futile.options generics GenomicRanges ggbeeswarm ggdendro ggplot2 ggrepel glue gtable IRanges isoband labeling lambda.r lattice lifecycle limma magrittr MASS Matrix MatrixGenerics matrixStats notame openxlsx pcaMethods pillar pkgconfig purrr qpdf R6 RColorBrewer Rcpp rlang Rtsne S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect utf8 vctrs vipor viridisLite withr XVector zip

Non-targeted metabolomics visualization

Rendered fromNon_targeted_metabolomics_visualization.Rmdusingknitr::rmarkdown

Last update: 2025-10-03
Started: 2025-09-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Manhattan plot	manhattan_plot
Plot m/z vs retention time plot (cloud plot)	mz_rt_plot
Sample dendrogram	plot_dendrogram
Plot distance density	plot_dist_density
Heatmap of effects between variables, such as correlations	plot_effect_heatmap
Estimate the magnitude of drift	plot_injection_lm
Histogram of p-values	plot_p_histogram
PCA scatter plot	plot_pca
PCA plot with arrows	plot_pca_arrows
PCA hexbin plot	plot_pca_hexbin
PCA loadings plot	plot_pca_loadings
Plot quality metrics	plot_quality
Plot a boxplot for each sample	plot_sample_boxplots
Sample heatmap	plot_sample_heatmap
t-SNE scatter plot	plot_tsne
t-SNE plot with arrows	plot_tsne_arrows
t-SNE hexbin plot	plot_tsne_hexbin
Save batch correction plots	save_batch_plots
Save beeswarm plots of each feature by group	save_beeswarm_plots
Save drift correction plots	save_dc_plots
Save box plots of each feature by group	save_group_boxplots
Save line plots with errorbars by group	save_group_lineplots
Save plot to chosen format	save_plot
Write all relevant pretreatment visualizations to pdf	save_QC_plots
Save scatter plots of each feature against a set variable	save_scatter_plots
Save line plots with mean	save_subject_line_plots
Visualize clusters of features	visualize_clusters
Volcano plot	volcano_plot