Nuclei Analysis Toolkit

Analysis summary

qc_table <- as.data.frame(attr(metadata, "de_params"))
datatable(qc_table, colnames = "", options = list(pageLength = 5))

Differential gene expression was performed on a total of r prettyNum(as.numeric(attr(metadata, "de_params")["n_genes"]),big.mark=",",scientific=FALSE) genes which expressed a minimum of r as.numeric(attr(metadata, "de_params")["min_counts"]) count in at least r as.numeric(attr(metadata, "de_params")["min_cells_pc"])*100 percent of the cells. Differentially expressed genes (DEGs) were detected at a fold-change threshold of r as.numeric(attr(metadata, "report_params")["fc_threshold"]) and an adjusted p-value (padj) cut-off of r as.numeric(attr(metadata, "report_params")["pval_cutoff"]) was applied.

Result summary

Up <- as.numeric(attr(metadata, "de_result")["Up"])
Down <- as.numeric(attr(metadata, "de_result")["Down"])
Total_gene <- as.numeric(attr(metadata, "de_params")["n_genes"])
Up_percent <- Up/Total_gene*100
Down_percent <- Down/Total_gene*100

r sprintf("\n\n**Up-regulated:** %g (%g%%) \n\n", Up, Up_percent)
r sprintf("\n\n**Down-regulated:** %g (%g%%) \n\n", Down, Down_percent)

Volcano plot

metadata_plot <- attr(metadata, "plot")

wzxhzdk:3

List of differentially expressed gene

fc_threshold <- as.numeric(attr(metadata, "report_params")["fc_threshold"]) 

pval_cutoff <- as.numeric(attr(metadata, "report_params")["pval_cutoff"])

#metadata_table <- metadata
metadata_table <- metadata %>%
  dplyr::filter(!is.na(padj)) %>%
  dplyr::filter(!is.nan(logFC)) %>%
  dplyr::filter(padj <= pval_cutoff, abs(logFC) >= log2(fc_threshold)) %>%
  dplyr::mutate_at(c("pval", "logFC", "ci.hi", "ci.lo", "padj"), ~ as.numeric(format(., format = "e", digits = 2))) %>%
  dplyr::mutate_at("variance", ~ round(., 2))
# metadata_table$pval <- as.numeric(format(metadata_table$pval, format = "e", digits = 2))
# metadata_table$logFC <- as.numeric(format(metadata_table$logFC, format = "e", digits = 2))
# metadata_table$ci.hi <- as.numeric(format(metadata_table$ci.hi, format = "e", digits = 2))
# metadata_table$ci.lo <- as.numeric(format(metadata_table$ci.lo, format = "e", digits = 2))
# metadata_table$padj <- as.numeric(format(metadata_table$padj, format = "e", digits = 2))
datatable(metadata_table, rownames = FALSE, options = list(pageLength = 10, scrollX=T, autoWidth = TRUE, columnDefs = list(list(width = '500px', targets = 12))), escape = FALSE )