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Jam SummarizedExperiment Stats (jamses)

This package is under active development. These functions are in frequent use in active Omics analysis projects. A summary of goals and relevant features are described below.

Jamses Online Documentation

Goals of jamses

The core goal is to make data analysis and visualization of SummarizedExperiment objects straightforward for common scenarios. It also accepts SingleCellExperiment and Seurat objects.

  • Make Effective Heatmaps

  • Apply Normalization / Adjustment

  • SEDesign: Create Design and Contrast matrices

    • Use ~ 0 + group syntax, see below.
    • Integrate Samples, Groups, and Contrasts.
    • Visualize with plot_sedesign().

  • SEStats: Analyze Multiple Contrasts

    • Use limma / limma-voom / limma-DEqMS.

  • Convenient contrast labels

     Contrast:
 `(Knockout_treated-Knockout_control)-(Wildtype_treated-Wildtype_control)`

 Comp:
 `Knockout-Wildtype:treated-control`

  • Integrate with other tools.

    • SummarizedExperiment, SingleCellExperiment, Seurat, ExpressionSet, DESeqDataset, DGElist
    • venndir::venndir() - see Github "jmw86069/venndir" to create directional Venn diagrams.

Make Effective Heatmaps

How to Make a Heatmap

Jamses heatmap_se() reinforces heatmap principles, and applies some opinions.

  • Data are centered.
  • Always use divergent colors for centered data.
  • Data are not scaled.
  • Row and Column annotations are “easy”.

Approach for Statistical Contrasts

The Limma User’s Guide (LUG) is an amazing resource which describes numerous approaches for one-way and two-way contrasts which are mathematically equivalent. For a more thorough discussion please review these approaches to confirm that ~0 + x is mathematically identical to ~ x, and only differs in how estimates are reported.

  • Jamses uses the ~0 + x strategy.

  • Each experiment group is defined using independent replicates.

  • This approach does not imply that there is “no intercept” during the model fit, see LUG for details.

  • One-way contrasts compare only one factor per contrast.

    • Valid one-way contrast:
    (A_treated - A_control) # valid one-way contrast
    • Invalid one-way contrast:
    (A_treated - B_control) # not a valid one-way contrast

  • Two-way contrasts in Jamses compare the fold change of two compatible one-way fold changes.

    • Two compatible one-way contrasts:
    (A_treated - A_control)  # one-way contrast
                         # "treated-control" for A
(B_treated - B_control)  # compatible one-way contrast
                         # "treated-control" for B
    • Corresponding two-way contrast:
    (B_treated - B_knockout) # incompatible one-way contrast

SEDesign: Design and Contrasts

  • groups_to_sedesign() takes by default a data.frame where each column represents an experiment factor, and creates the following:
  • Output is SEDesign as an S4 object with slot names:
    • design(sedesign) - the design matrix.
    • contrasts(sedesign) - the contrasts matrix.
    • samples(sedesign) - vector of samples.

Example SEDesign object

The example below uses a character vector of group names per sample, with two factors separated by underscore "_". The same data can be provided as a data.frame with two columns.

library(jamses)

igroups <- jamba::nameVector(paste(rep(c("WT", "KO"), each=6),
   rep(c("Control", "Treated"), each=3),
   sep="_"),
   suffix="_rep");
igroups <- factor(igroups, levels=unique(igroups));

jamba::kable_coloring(color_cells=FALSE,
   caption="Sample to group association",
   data.frame(groups=igroups))
Sample to group association
groups
WT_Control_rep1 WT_Control
WT_Control_rep2 WT_Control
WT_Control_rep3 WT_Control
WT_Treated_rep1 WT_Treated
WT_Treated_rep2 WT_Treated
WT_Treated_rep3 WT_Treated
KO_Control_rep1 KO_Control
KO_Control_rep2 KO_Control
KO_Control_rep3 KO_Control
KO_Treated_rep1 KO_Treated
KO_Treated_rep2 KO_Treated
KO_Treated_rep3 KO_Treated

The resulting design and contrasts matrices are shown below:

sedesign <- groups_to_sedesign(igroups);
jamba::kable_coloring(
   colorSub=c(`-1`="dodgerblue", `1`="firebrick"),
   caption="Design matrix output from design(sedesign).",
   data.frame(check.names=FALSE, design(sedesign)));
Design matrix output from design(sedesign).
WT_Control WT_Treated KO_Control KO_Treated
WT_Control_rep1 1 0 0 0
WT_Control_rep2 1 0 0 0
WT_Control_rep3 1 0 0 0
WT_Treated_rep1 0 1 0 0
WT_Treated_rep2 0 1 0 0
WT_Treated_rep3 0 1 0 0
KO_Control_rep1 0 0 1 0
KO_Control_rep2 0 0 1 0
KO_Control_rep3 0 0 1 0
KO_Treated_rep1 0 0 0 1
KO_Treated_rep2 0 0 0 1
KO_Treated_rep3 0 0 0 1 

jamba::kable_coloring(
   colorSub=c(`-1`="dodgerblue", `1`="firebrick"),
   caption="Contrast matrix output from contrasts(sedesign).",
   data.frame(check.names=FALSE, contrasts(sedesign)));
Contrast matrix output from contrasts(sedesign).
KO_Control-WT_Control KO_Treated-WT_Treated WT_Treated-WT_Control KO_Treated-KO_Control (KO_Treated-WT_Treated)-(KO_Control-WT_Control)
WT_Control -1 0 -1 0 1
WT_Treated 0 -1 1 0 -1
KO_Control 1 0 0 -1 -1
KO_Treated 0 1 0 1 1

For convenience, SEDesign can be visualized using plot_sedesign():

# plot the design and contrasts
plot_sedesign(sedesign);
title(main="plot_sedesign(sedesign):")

  • One-way contrasts are shown with a wide block arrow.

  • Two-way contrasts are shown by connecting two block arrows with a “squiggly curved line”.

    • It connects the end of one contrast
      to the beginning of the next contrast.
    • The order indicates that the first contrast is subtracted by the second contrast.