Package index

SomaLogic `ggplot2`-style

Use themes, palettes, and scales to generate ggplots with consistent style and format.

palette_soma() scale_color_soma() scale_fill_soma() scale_continuous_color_soma() scale_continuous_fill_soma(): SomaLogic Primary Color Palette

theme_soma(): SomaLogic ggplot2 Theme

palette_soma_gender() scale_color_soma_gender() scale_fill_soma_gender(): SomaLogic Sex/Gender Color Palette

palette_soma_greys() scale_color_soma_greys() scale_fill_soma_greys(): SomaLogic Greyscale Color Palette

palette_soma_risk() scale_color_soma_risk() scale_fill_soma_risk() scale_continuous_color_soma_risk() scale_continuous_fill_soma_risk(): SomaLogic Risk Category Color Palette

Concordance

Plotting concordance of two continuous variables.

plotConcord(): Plot Concordance

CDFs and PDFs

Plotting cumulative distribution functions (CDF) and probability density functions (PDF).

addCDFquantiles(): Add Quantile Lines to CDF Plot

plotCDF() plotCDFbyGroup() plotCDFlist(): Plots an Empirical CDF

plotPDF() plotPDFbyGroup() plotPDFlist(): Plot PDF of Empirical Data

Volcano Plots

Plotting volcanos.

plotVolcano(): Create Volcano Plot

plotVolcanoHTML(): Generate HTML-based Volcano Plot

Longitudinal data

Plotting time series or longitudinal traces.

plotLongitudinal(): Plot Longitudinal Samples by Subject

plotPolygon() addPolygon(): Plot a Polygon Shaded Area

Boxplot graphics

Various forms of boxplots.

boxplotBeeswarm(): Create a "Beeswarm" Boxplot

boxplotGrouped(): Grouped Boxplots by Factor(s)

boxplotSubarray(): Plot Boxplots by Subarray (Sample)

Maps

Plotting maps; “fold-change”, “outlier”, and “missingness”.

SomaPlotr-deprecated calcOutlierMap deprecated: Deprecated function(s) of the SomaPlotr package

calcFoldchangeMatrix() print(<foldchange_matrix>): Calculate Fold-Change Matrix

calcMissingnessMap() print(<missingness_map>): Calculate Missingness of Clinical Meta Data

plot(<Map>): Plot Image Maps

getFlaggedIds(): Get Flagged Ids From MAD Outlier or Missingness Maps

Histograms

Various forms of histograms.

plotDoubleHist(): Plot a Double-Histogram

Exporting base plots

Useful utilities to save plots to file.

figure() close_figure(): Saves a Figure (Plot) to File

Package Data

Data objects in SomaPlotr.

soma_colors2 soma_colors soma_colors_risk soma_colors_greys soma_blue soma_purple col_string gg: SomaPlotr Colors and Graphics

SomaLogic ggplot2-style