data_ref: Calculating relative expression values

In jianhaizhang/spatialHeatmap: spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

Calculating relative expression values

Description

This function computes relative expression values for plotting spatial heatmaps (SHMs).

Usage

data_ref(se, input.log, output.log = TRUE)

Arguments

se	A 'SummarizedExperiment' object containing non-log-transformed data. The 'colData' slot contains a minimum of three columns: 'spFeature' (spatial feature), 'variable' (experiment variable), and 'reference' (reference variable). The first two columns are explained in the 'data' argument of the filter_data function. The 'reference' indicates reference experimental variables that are comma-separated strings such as "variable1,variable2" (see the example below). Relative expression values will be computed based on the references.
input.log	Logical, 'TRUE' or 'FALSE', indicating whether the input assay data are log-transformed or not, repectively. If 'TRUE' this function will not compute relative expression values, since the log-transformed values significantly reduces real relative expression levels. Users are expected to ensure the input assay data are non-log-transformed and then select 'FALSE'.
output.log	Logical. If 'FALSE', the output relative expression values are ratios such as treatment/control, while if 'TRUE', it would be log2 fold changes such as log2(treatment/control).

Value

A 'SummarizedExperiment' object that contains relative expression values.

Author(s)

Jianhai Zhang [e-mail]

References

Morgan M, Obenchain V, Hester J, Pagès H (2022). SummarizedExperiment: SummarizedExperiment container. R package version 1.28.0, <https://bioconductor.org/packages/SummarizedExperiment>. R Core Team (2018). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/ Cardoso-Moreira, Margarida, Jean Halbert, Delphine Valloton, Britta Velten, Chunyan Chen, Yi Shao, Angélica Liechti, et al. 2019. “Gene Expression Across Mammalian Organ Development.” Nature 571 (7766): 505–9

Examples

library(SummarizedExperiment)
# Access example data. 
se <- readRDS(system.file('extdata/shinyApp/data/mouse_organ.rds',
package='spatialHeatmap'))
colData(se)[1:4, 1:3]; assay(se)[1:3, 1:3]
# Data of relative expression values.
se.ref <- data_ref(se, input.log=FALSE)
colData(se.ref)[, 1:3]; assay(se.ref)[1:3, 1:3]

jianhaizhang/spatialHeatmap documentation built on Nov. 28, 2024, 4:44 p.m.