plotHeatmapPretrained {MetaNeighbor}R Documentation

Plots rectangular AUROC heatmap, clustering train cell types (columns) by similarity, and ordering test cell types (rows) according to similarity to train cell types..

Description

Plots rectangular AUROC heatmap, clustering train cell types (columns) by similarity, and ordering test cell types (rows) according to similarity to train cell types..

Usage

plotHeatmapPretrained(
  aurocs,
  alpha_col = 1,
  alpha_row = 10,
  cex = 1,
  margins = c(8, 8)
)

Arguments

aurocs

A rectangular AUROC matrix as returned by MetaNeighborUS,

alpha_col

Parameter controling column clustering: a higher value of alpha_col gives more weight to extreme AUROC values (close to 1).

alpha_row

Parameter controling row ordering: a higher value of alpha_row gives more weight to extreme AUROC values (close to 1).

cex

Size factor for row and column labels.

margins

Size of margins (for row and column labels).

Examples

data(mn_data)
var_genes = variableGenes(dat = mn_data, exp_labels = mn_data$study_id)
celltype_NV = MetaNeighborUS(var_genes = var_genes,
                             dat = mn_data,
                             study_id = mn_data$study_id,
                             cell_type = mn_data$cell_type,
                             symmetric_output = FALSE)
keep_col = getStudyId(colnames(celltype_NV)) == "GSE71585"
keep_row = getStudyId(rownames(celltype_NV)) != "GSE71585"
plotHeatmapPretrained(celltype_NV[keep_row, keep_col])


[Package MetaNeighbor version 1.14.0 Index]