Panel Catalogue

Giulio Benedetti

University of Turku

10 March 2025

Source: vignettes/panels.Rmd

Introduction

This page introduces users to the complete catalogue of panels provided by iSEEtree. Each panel is presented individually and visualised as it appears in the app. This catalogue is divided into four sections:

  • compositional analysis: abundance plot, abundance density plot, prevalence plot and complex heatmap plot
  • ordination analysis: RDA plot, Scree plot, loading plot and reduced dimension plot
  • structural analysis: row/column tree plots and row/column graph plots
  • other: row/column tile plots, mediation plot and row/column data plots

Compositional Analysis

Panel name Panel class Purpose
Abundance plot AbundancePlot Feature composition by sample
Abundance density plot AbundanceDensityPlot Feature distribution across samples
Prevalence plot PrevalencePlot Feature prevalence across samples
Complex heatmap plot ComplexHeatmapPlot Whole assay composition

Abundance plot

The Abundance plot illustrates the feature composition of each sample with a barplot of the relative or absolute feature abundace. This panel is based on the miaViz function plotAbundance.

Supported operations:

  • Selecting taxonomic rank of the composition
  • Choosing either absolute or relative abundance
  • Ordering samples by feature or sample metadata
  • Customising aesthetics

Abundance density plot

The Abundance density plot provides an alternative way to visualise abundance. In this panel, each row represents the feature distribution across the samples. It is based on the miaViz function plotAbundanceDensity.

Supported operations:

  • selecting layout (jitter, density or dot plot)
  • specifying the number of top features to show
  • customising aesthetics

Prevalence plot

Coming soon!

Complex heatmap plot

Ordination Analysis

Panel name Panel class Purpose
RDA plot RDAPlot Supervised ordination
Scree plot ScreePlot Explained variance by component
Loading plot LoadingPlot Feature loadings by component
Reduced dimension plot ReducedDimensionPlot Any ordination result

RDA plot

The RDA plot visualises results for a distance-based Redundance Analysis (dbRDA) performed on a TreeSE object with the mia function runRDA. It is based on the miaViz function plotRDA.

Supported operations:

  • selecting reduced dimension
  • adjusting statistical parameters
  • customising aesthetics

Scree plot

The Scree plot shows the proportion of variance explained by each component of a dimensionality reduction analysis by means of a line plot or barplot. It is based on the miaViz function plotScree.

Supported operations:

  • selecting reduced dimension
  • changing number of components
  • showing individual or cumulative variance
  • adding components labels and names

Loading plot

The Loading plot visualises the contributions of each feature to the components of a reduced dimension of choice. It is based on the miaViz function plotLoadings.

Supported operations:

  • selecting layout (barplot, heatmap or lollipop)
  • changing number of components
  • adding feature tree

Reduced dimension plot

The Reduced dimension plot is inherited from iSEE. It is based on the scater function plotReducedDim and and can be used to visualise the results of an ordination analysis with both supervised and unsupervised methods as dot plot with reduced dimensions as coordinate axes.

Structural Analysis

Panel name Panel class Purpose
Row tree plot RowTreePlot Hierarchical structure of features
Column tree plot ColumnTreePlot Hierarchical structure of samples
Row graph plot RowGraphPlot Network structure of features
Column graph plot ColumnGraphPlot Network structure of samples

Row/Column tree plots

Row and column tree plots belong to the TreePlot family. They can be used to visualise the hierarchical organisation of the features or samples by means of a tree. They are based on the miaViz functions plotRowTree and plotColTree.

Supported operations:

  • collapsing and expanding clades
  • rotating and opening trees
  • ordering trees
  • labeling nodes and tips
  • selecting tree layout
  • customising aesthetics

Row/Column graph plots

Row and column graph plots belong to the GraphPlot family. They can be used to visualise the network organisation of the features or samples by means of a graph. They are based on the miaViz functions plotRowGraph and plotColGraph.

Supported operations:

  • selecting graph and assay type
  • labelling nodes
  • selecting graph layout
  • selecting edge type
  • customising aesthetics

Other panels

Panel name Panel class Purpose
Row tile plot RowTreePlot Variable distribution across feature groups
Column tile plot ColumnTreePlot Variable distribution across sample groups
Mediation plot MediationPlot Results of mediation analysis
Row data plot RowDataPlot Variables from feature metadata
Column data plot ColumnDataPlot Variables from sample metadata

Row/Column tile plots

Coming soon!

Mediation plot

Coming soon!

Row/Column data plots

The Row and column data plots are inherited from iSEE. They are based on the scater functions plotRowData and plotColData and can be used to visualise feature or sample metadata as scatter plots when the x variable is continuous or boxplots when the x variable is discrete.

Reproducibility

R session information:

#> R Under development (unstable) (2025-03-04 r87880)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.1 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] BiocStyle_2.35.0
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.37       desc_1.4.3          R6_2.6.1            bookdown_0.42       fastmap_1.2.0      
#>  [6] xfun_0.51           cachem_1.1.0        knitr_1.49          htmltools_0.5.8.1   rmarkdown_2.29     
#> [11] lifecycle_1.0.4     cli_3.6.4           sass_0.4.9          pkgdown_2.1.1       textshaping_1.0.0  
#> [16] jquerylib_0.1.4     systemfonts_1.2.1   compiler_4.5.0      tools_4.5.0         ragg_1.3.3         
#> [21] evaluate_1.0.3      bslib_0.9.0         yaml_2.3.10         BiocManager_1.30.25 jsonlite_1.9.1     
#> [26] rlang_1.1.5         fs_1.6.5            htmlwidgets_1.6.4

References