1 Getting started

The sechm package is a wrapper around the ComplexHeatmap package to facilitate the creation of annotated heatmaps from objects of the Bioconductor class SummarizedExperiment (and extensions thereof).

1.1 Package installation

if (!requireNamespace("BiocManager", quietly = TRUE))

1.2 Example data

To showcase the main functions, we will use an example object which contains (a subset of) RNAseq of mouse hippocampi after Forskolin-induced long-term potentiation:

data("Chen2017", package="sechm")
SE <- Chen2017

This is taken from Chen et al., 2017.

2 Example usage

2.1 Basic functionalities

The sechm function simplifies the generation of heatmaps from SummarizedExperiment. It minimally requires, as input, a SummarizedExperiment object and a set of genes (or features, i.e. rows of sechm) to plot:

g <- c("Egr1", "Nr4a1", "Fos", "Egr2", "Sgk1", "Arc", "Dusp1", "Fosb", "Sik1")
sechm(SE, features=g)
## Using assay 'logFC'

# with row scaling:
sechm(SE, features=g, do.scale=TRUE)
## Using assay 'logFC'

The assay can be selected, and any rowData or colData columns can be specified as annotation:

rowData(SE)$meanLogCPM <- rowMeans(assays(SE)$logcpm)
sechm(SE, features=g, assayName="logFC", top_annotation=c("Condition","Time"), left_annotation=c("meanLogCPM"))

Column names are ommitted by default, but can be displayed:

sechm(SE, features=g, do.scale=TRUE, show_colnames=TRUE)
## Using assay 'logFC'

Since sechm uses the ComplexHeatmap engine for plotting, any argument of ComplexHeatmap::Heatmap can be passed:

sechm(SE, features=g, do.scale=TRUE, row_title="My genes")
## Using assay 'logFC'

When plotting a lot of rows, by default row names are not shown (can be overriden), but specific genes can be highlighted with the mark argument:

sechm(SE, features=row.names(SE), mark=g, do.scale=TRUE, top_annotation=c("Condition","Time"))
## Using assay 'logFC'

We can also add gaps using the same columns:

sechm(SE, features=g, do.scale=TRUE, top_annotation="Time", gaps_at="Condition")
## Using assay 'logFC'

2.2 Row ordering

By default, rows are sorted using the MDS angle method (can be altered with the sort.method argument); this can be disabled with:

# reverts to clustering:
sechm(SE, features=row.names(SE), do.scale=TRUE, sortRowsOn=NULL)
## Using assay 'logFC'