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...
        scale_y_log10(
            guide = guide_axis_logticks(long = 1.5, mid = 1.0, short = 0.5),
            breaks = c(0.001, 0.01, 0.1, 1.00), limits = c(0.001, 1), expand = c(0, 0)
        ) +
        scale_x_log10(
            guide = guide_axis_logticks(long = 1.5, mid = 1.0, short = 0.5),
            breaks = c(0.001, 0.01, 0.1, 1.00), limits = c(0.001, 1), expand = c(0, 0)
        ) +
...

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LINE.W <- 0.232 # 0.5pt

breaks_log10 <- function(x) {
    low <- floor(log10(min(x)))
    high <- ceiling(log10(max(x)))
    10^(seq.int(low, high))
}

... scale_y_log10(
            limits = c(1e-3, 10),

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# premessa::concatenate_fcs_files
# modified based on the following code:
# https://rdrr.io/github/ParkerICI/premessa/src/R/fcs_io.R

update_flowFrame_keywords <- function(flowFrame, exprs.m, desc = NULL, data.range = "data") {
    params <- flowCore::parameters(flowFrame)
    pdata <- flowCore::pData(params)

    if (is.null(desc)) {
        desc <- colnames(exprs.m)

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compute_dynamic_gate <- function(gs, inv.bins) {
    df.stat <- data.frame()
    for (min.cutoff in inv.bins) {
        # Create dynamic FL1-A gate
        rg_gfp <- flowCore::rectangleGate(
            "FL1-A" = c(min.cutoff, Inf), "FSC-A" = c(-Inf, Inf),
            filterId = "_dynamic"
        )
        gates <- flowWorkspace::gs_get_pop_paths(gs)
        if ("/P1/_dynamic" %in% gates) {

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{
    //Theme
    "workbench.colorTheme": "Monokai Dimmed",

    //Editor configs
    "files.autoSave": "afterDelay",
    "editor.minimap.enabled": false,
    "workbench.colorCustomizations": {"editorIndentGuide.background": "#00000000" }, // hide via 100% transparency.
    "git.ignoreLegacyWarning": true,
    "workbench.editor.enablePreview": false,

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...
sample.names <- sampleNames(gs.trans)
gs.exp.df <- data.table()
for (sample in sample.names) {
    message(sprintf("Processing: %s", sample))
    df <- gs_get_singlecell_expression(gs.trans, c("P1"),
        threshold = FALSE, marginal = FALSE, inverse.transform = TRUE,
        other.markers = c("SSC-A", "FL1-A", "FL5-A")
    )[[sample]] %>%
        data.table() %>%

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{
    "init_knit": {
        "prefix": "init_knit",
        "body": [
            "---",
            "title: $1",
            "author: \"Soh Ishiguro\"",
            "date: \"`r Sys.Date()`\"",
            "output:",
            "  html_document: ",

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---
title: "notebook title"
author: "Soh Ishiguro"
date: "`r Sys.Date()`"
output:
  html_document: 
    toc: yes
    toc_float: no
    number_sections: yes
    keep_md: yes

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/*
  Edit this CSS file to change styles of the editor.
  If you need to revert it back, use the "Reset" button.
*/

/**
* Text Cell
*/

.text-cell {

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module main

using BioSequences
using BioAlignments
using BenchmarkTools

struct AlignmentResults
    align::BioAlignments.PairwiseAlignmentResult
    name::String
end