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