Evaluate n_bins and n_genes for bin mapping — evaluate

Will use the n_bins and n_genes implied by the sce and pseudotime_bins_top_n_genes_df parameters and return quality metrics and an optional chart.

Usage

evaluate_parameters(
  blase_data,
  bootstrap_iterations = 200,
  BPPARAM = BiocParallel::SerialParam(),
  make_plot = FALSE,
  plot_columns = 4
)

Arguments

blase_data

The BlaseData object to use.

bootstrap_iterations

Iterations for bootstrapping when calculating confident mappings.

BPPARAM

The BiocParallel configuration. Defaults to SerialParam.

make_plot

Whether or not to render the plot showing the correlations for each pseudobulk bin when we try to map the given bin.

plot_columns

How many columns to use in the plot.

.@import patchwork

Value

A vector of length 3:

"worst top 2 distance" containing the lowest difference between the absolute values of the top 2 most correlated bins for each bin. Higher is better for differentiating.
"mean top 2 distance" containing the mean top 2 distance across the entire set of genes and bins. Higher is better for differentiation, but it should matter less than the worst value.
"confident_mapping_pct" - The percent of mappings for this setup which were annotated as confident by BLASE

Examples

ncells <- 70
ngenes <- 100
counts_matrix <- matrix(
    c(seq_len(3500) / 10, seq_len(3500) / 5),
    ncol = ncells,
    nrow = ngenes
)
sce <- SingleCellExperiment::SingleCellExperiment(assays = list(
    normcounts = counts_matrix, logcounts = log(counts_matrix)
))
colnames(sce) <- seq_len(ncells)
rownames(sce) <- as.character(seq_len(ngenes))
sce$cell_type <- c(
    rep("celltype_1", ncells / 2),
    rep("celltype_2", ncells / 2)
)

sce$pseudotime <- seq_len(ncells) - 1
genelist <- as.character(seq_len(ngenes))

# Evaluating created BlaseData
blase_data <- as.BlaseData(sce, pseudotime_slot = "pseudotime", n_bins = 10)
genes(blase_data) <- genelist[1:20]

# Check convexity of parameters
evaluate_parameters(blase_data, make_plot = TRUE)
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:1
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:1
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:2
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:3
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:3
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:3
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:4
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:4
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:4
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:4
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:5
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:5
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:5
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:5
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:5
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:5
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:5
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:5
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:6
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:6
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:7
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:7
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:7
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:7
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:7
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:7
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:7
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:8
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:8
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:8
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:8
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:8
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:8
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:8
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:9
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:9
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:9
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:9
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:9
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:9
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#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:10
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:10
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:10
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:10
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:10
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:10
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:10
#> Warning: Bulk ID matches a gene, if this fails then check you areusing bulk name and not geneIds:10
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