sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.
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sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible.
library(SummarizedExperiment)
library(sechm)
# Load example data
data("Chen2017", package="sechm")
SE <- Chen2017
# 1. Basic scaled heatmap of top variable genes
g <- c("Egr1", "Nr4a1", "Fos", "Egr2", "Sgk1", "Arc", "Dusp1", "Fosb", "Sik1")
sechm(SE, features=g, do.scale=TRUE)
# 2. Heatmap of Log2 Fold Changes with quantile capping (breaks)
sechm(SE, features=g, assayName="logFC", breaks=0.985)
# 3. Customizing colors using global package options
setSechmOption("hmcols", value=c("white","grey","black"))
sechm(SE, features=g, do.scale=TRUE)
resetAllSechmOptions()
Input: A SummarizedExperiment object and a vector of feature names. Output: A Heatmap object from ComplexHeatmap.
SummarizedExperiment objects using sechm().rowData and colData (e.g., top_annotation, left_annotation).SummarizedExperiment objects with aligned rows and consistent scales using crossHm().mark argument.SummarizedExperiment container, use ComplexHeatmap::Heatmap or pheatmap directly.SummarizedExperiment object containing at least one assay (e.g., "logcpm", "logFC").rowData(SE) and column annotations stored in colData(SE)."logFC").FALSE): Logical indicating whether to scale rows.colData to display as top annotations.rowData to display as left annotations.TRUE): Controls symmetric scaling and quantile capping (e.g., 0.985 for 98.5% quantile capping).colData to introduce gaps between columns.FALSE): Logical indicating whether to enforce a unique color scale across datasets in crossHm().metadata(SE)$default_view to simplify repetitive plotting.breaks=0.985) when plotting fold-changes to prevent extreme outlier values from dominating the color scale.metadata(SE)$anno_colors to ensure they are automatically applied across all heatmaps generated from that object.breaks to a quantile value less than 1 (e.g., breaks=0.985) to cap the color scale.+: Combining raw sechm objects can lead to conflicts. Fix: Use crossHm() to safely plot multiple SummarizedExperiment objects side-by-side.ComplexHeatmap: The underlying engine, but requires manual extraction of assays and annotations from SummarizedExperiment.pheatmap: A classic heatmap package, but lacks native integration with SummarizedExperiment metadata.还没有评价。欢迎分享你的使用感受。
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