HeatmapDiag: HeatmapDiag utility function for 'pheatmap' using 'slanter'...

In MattPM/scglmmr: Sample-level Single-cell Generalized Linear Multilevel Models in R

HeatmapDiag utility function for 'pheatmap' using 'slanter' to order the maximum values across the matrix diagonal

Description

HeatmapDiag utility function for 'pheatmap' using 'slanter' to order the maximum values across the matrix diagonal

Usage

HeatmapDiag(matrix, ...)

Arguments

matrix

an R matrix as input to 'pheatmap'. Could be the object returned by 'scglmmr::GetGeneMatrix'

Value

a pheatmap object

Examples

## Not run: 
# make gene plot of top 50 ranked genes within each subst
# fit1 = dreamMixedModel(...)
r1 = ExtractResult(model.fit.list = fit1, coefficient.number = 1,coef.name = 'L1', what = 'gene.t.ranks')
rank = lapply(r1,function(x) names(x[1:50]))
top50ranks = unlist(rank) %>% unique()
res1 = ExtractResult(model.fit.list = fit1, coefficient.number = 1,coef.name = 'L1')
mtx = GetGeneMatrix(result.list = res1, gene_subset = top50ranks, stat_for_matrix = 'logFC', pvalfilter = 1, logfcfilter = -Inf)
pdf(file = paste0(figpath, 'geneplot.pdf'), width = 3.5 ,height = 5)
HeatmapDiag(matrix = mtx, fontsize_row = 1)
dev.off()

## End(Not run)

MattPM/scglmmr documentation built on April 26, 2024, 12:55 a.m.