Htmlwidgets Binding R Commands to The BioCircos.js Library

BioCircos.R

Simple htmlwidgets binding R commands to the BioCircos.js library

---

Introduction

This package allows to implement in 'R' Circos-like visualizations of genomic data, as proposed by the BioCircos.js JavaScript library, based on the JQuery and D3 technologies.
For a complete list of all the parameters available, please refer to the package documentation.

Motivation

The amount of data produced nowadays in a lot of different fields assesses the relevance of reactive analyses and interactive display of the results. This is especially true in biology, where the cost of sequencing data has dropped must faster than the Moore's law prediction. New ways of integrating different levels of information and accelerating the interpretation are therefore needed.

The integration challenge appears to be of major importance, as it allows a deeper understanding of the biological phenomena happening, that cannot be observed in the single analyses independently.

This package aims at offering an easy way of producing Circos-like visualizations to face distinct challenges :

• On the one hand, data integration and visualization: Circos is a popular tool to combine different biological information on a single plot.
• On the other hand, reactivity and interactivity: thanks to the htmlwidgets framework, the figures produced by this package are responsive to mouse events and display useful tooltips, and they can be integrated in shiny apps. Once the analyses have been performed and the shiny app coded, it is possible for the end-user to explore a massive amount of biological data without any programming or bioinformatics knowledge.

The terminology used here arises from genomics but this tool may be of interest for different situations where different positional or temporal informations must be combined.

Installation

To install this package, you can use CRAN (the central R package repository) to get the last stable release or build the last development version directly from the GitHub repository.

From CRAN

install.packages('BioCircos')

From Github

# You need devtools for that
if (!require('devtools')){install.packages('devtools')}
devtools::install_github('lvulliard/BioCircos.R', build_vignettes = TRUE))

Compatibility and troubleshooting

Since the visualizations are powered by JavaScript, they are affected by the environment in which they are displayed.

• If nothing shows up in the Rstudio viewer pane, try displaying the plot you generated in your browser instead. You can export the figure using the Save as Web Page... option in the Export tab of the viewer pane.
• If nothing shows up in a shiny application or an Rmarkdown document, try to update your web browser. See the vignettes for examples of BioCircos plots that should be correctly displayed.
• Rotation of labels using the genomeLabelOrientation parameter leads to a slight offset of the text when displayed in Firefox because some recent CSS options are not yet implemented.

Obseved behavior

• Firefox 55, Chrome 54 and later versions work as expected.
• Firefox 46, Chrome 53 and past versions do not display the plots at all.
• Firefox 47 to 54 do not include all features, such as zooming.

Tutorial

See the vignettes to learn how to use BioCircos visualizations.

vignette('BioCircos')

Original work

BioCircos.js : an Interactive Circos JavaScript Library for Biological Data Visualization on Web Applications.

https://github.com/YaCui/Biocircos.js

http://bioinfo.ibp.ac.cn/biocircos/

http://www.ncbi.nlm.nih.gov/pubmed/26819473

Documentation: http://bioinfo.ibp.ac.cn/biocircos/document/index.html

Modifications

The following features have been added to the original BioCircos.js library, based on version 1.1.2:

• Parameter snp_value_maxmin_instance set by SNPsettings.range when provided, to allow the use of a pre-defined range of values for the SNP track.
• Similar parameters added for the range of Histogram/Bar tracks, Line tracks, CNV tracks and Heatmap tracks (for the range to be used for color mapping).
• Parameter opacity added to each elements of SNP and Arc tracks.
• Changes were made in order to allow rotation of genome labels with the new parameter genomeLabelOrientation and the radial offset dy is now directly integrated in the label translation.

Contact

To report bugs, request features or for any question or remark regarding this package, please use the GitHub page or contact Loan Vulliard.

Credits

The creation and implementation of the BioCircos.js JavaScript library is an independent work attributed to Ya Cui and Xiaowei Chen.
This work is described in the following scientific article: BioCircos.js: an Interactive Circos JavaScript Library for Biological Data Visualization on Web Applications. Cui, Y., et al. Bioinformatics. (2016).

This package relies on several open source projects other R packages, and is made possible thanks to shiny and htmlwidgets.

The package heatmaply was used as a model for this vignette, as well as for the htmlwidgets configuration.

Download Details:

Author: lvulliard
Source Code: https://github.com/lvulliard/BioCircos.R 
License:  GPL-2.0 license

#r #shiny 

What is GEEK

Buddha Community

CSharp REPL: A Command Line C# REPL with Syntax Highlighting

C# REPL

A cross-platform command line REPL for the rapid experimentation and exploration of C#. It supports intellisense, installing NuGet packages, and referencing local .NET projects and assemblies.

 

(click to view animation)

C# REPL provides the following features:

• Syntax highlighting via ANSI escape sequences
• Intellisense with fly-out documentation
• Nuget package installation
• Reference local assemblies, solutions, and projects
• Navigate to source via Source Link
• IL disassembly (both Debug and Release mode)
• Fast and flicker-free rendering. A "diff" algorithm is used to only render what's changed.

Installation

C# REPL is a .NET 6 global tool, and runs on Windows 10, Mac OS, and Linux. It can be installed via:

dotnet tool install -g csharprepl

If you're running on Mac OS Catalina (10.15) or later, make sure you follow any additional directions printed to the screen. You may need to update your PATH variable in order to use .NET global tools.

After installation is complete, run csharprepl to begin. C# REPL can be updated via dotnet tool update -g csharprepl.

Usage:

Run csharprepl from the command line to begin an interactive session. The default colorscheme uses the color palette defined by your terminal, but these colors can be changed using a theme.json file provided as a command line argument.

Evaluating Code

Type some C# into the prompt and press Enter to run it. The result, if any, will be printed:

> Console.WriteLine("Hello World")
Hello World

> DateTime.Now.AddDays(8)
[6/7/2021 5:13:00 PM]

To evaluate multiple lines of code, use Shift+Enter to insert a newline:

> var x = 5;
  var y = 8;
  x * y
40

Additionally, if the statement is not a "complete statement" a newline will automatically be inserted when Enter is pressed. For example, in the below code, the first line is not a syntactically complete statement, so when we press enter we'll go down to a new line:

> if (x == 5)
  | // caret position, after we press Enter on Line 1

Finally, pressing Ctrl+Enter will show a "detailed view" of the result. For example, for the DateTime.Now expression below, on the first line we pressed Enter, and on the second line we pressed Ctrl+Enter to view more detailed output:

> DateTime.Now // Pressing Enter shows a reasonable representation
[5/30/2021 5:13:00 PM]

> DateTime.Now // Pressing Ctrl+Enter shows a detailed representation
[5/30/2021 5:13:00 PM] {
  Date: [5/30/2021 12:00:00 AM],
  Day: 30,
  DayOfWeek: Sunday,
  DayOfYear: 150,
  Hour: 17,
  InternalKind: 9223372036854775808,
  InternalTicks: 637579915804530992,
  Kind: Local,
  Millisecond: 453,
  Minute: 13,
  Month: 5,
  Second: 0,
  Ticks: 637579915804530992,
  TimeOfDay: [17:13:00.4530992],
  Year: 2021,
  _dateData: 9860951952659306800
}

A note on semicolons: C# expressions do not require semicolons, but statements do. If a statement is missing a required semicolon, a newline will be added instead of trying to run the syntatically incomplete statement; simply type the semicolon to complete the statement.

> var now = DateTime.Now; // assignment statement, semicolon required

> DateTime.Now.AddDays(8) // expression, we don't need a semicolon
[6/7/2021 5:03:05 PM]

Keyboard Shortcuts

• Basic Usage
  • Ctrl+C - Cancel current line
  • Ctrl+L - Clear screen
  • Enter - Evaluate the current line if it's a syntactically complete statement; otherwise add a newline
  • Control+Enter - Evaluate the current line, and return a more detailed representation of the result
  • Shift+Enter - Insert a new line (this does not currently work on Linux or Mac OS; Hopefully this will work in .NET 7)
  • Ctrl+Shift+C - Copy current line to clipboard
  • Ctrl+V, Shift+Insert, and Ctrl+Shift+V - Paste text to prompt. Automatically trims leading indent
• Code Actions
  • F1 - Opens the MSDN documentation for the class/method under the caret (example)
  • F9 - Shows the IL (intermediate language) for the current statement in Debug mode.
  • Ctrl+F9 - Shows the IL for the current statement with Release mode optimizations.
  • F12 - Opens the source code in the browser for the class/method under the caret, if the assembly supports Source Link.
• Autocompletion
  • Ctrl+Space - Open autocomplete menu. If there's a single option, pressing Ctrl+Space again will select the option
  • Enter, Right Arrow, Tab - Select active autocompletion option
  • Escape - closes autocomplete menu
• Text Navigation
  • Home and End - Navigate to beginning of a single line and end of a single line, respectively
  • Ctrl+Home and Ctrl+End - Navigate to beginning of line and end across multiple lines in a multiline prompt, respectively
  • Arrows - Navigate characters within text
  • Ctrl+Arrows - Navigate words within text
  • Ctrl+Backspace - Delete previous word
  • Ctrl+Delete - Delete next word

Adding References

Use the #r command to add assembly or nuget references.

• For assembly references, run #r "AssemblyName" or #r "path/to/assembly.dll"
• For project references, run #r "path/to/project.csproj". Solution files (.sln) can also be referenced.
• For nuget references, run #r "nuget: PackageName" to install the latest version of a package, or #r "nuget: PackageName, 13.0.5" to install a specific version (13.0.5 in this case).

To run ASP.NET applications inside the REPL, start the csharprepl application with the --framework parameter, specifying the Microsoft.AspNetCore.App shared framework. Then, use the above #r command to reference the application DLL. See the Command Line Configuration section below for more details.

csharprepl --framework  Microsoft.AspNetCore.App

Command Line Configuration

The C# REPL supports multiple configuration flags to control startup, behavior, and appearance:

csharprepl [OPTIONS] [response-file.rsp] [script-file.csx] [-- <additional-arguments>]

Supported options are:

• OPTIONS:
  • -r <dll> or --reference <dll>: Reference an assembly, project file, or nuget package. Can be specified multiple times. Uses the same syntax as #r statements inside the REPL. For example, csharprepl -r "nuget:Newtonsoft.Json" "path/to/myproj.csproj"
    • When an assembly or project is referenced, assemblies in the containing directory will be added to the assembly search path. This means that you don't need to manually add references to all of your assembly's dependencies (e.g. other references and nuget packages). Referencing the main entry assembly is enough.
  • -u <namespace> or --using <namespace>: Add a using statement. Can be specified multiple times.
  • -f <framework> or --framework <framework>: Reference a shared framework. The available shared frameworks depends on the local .NET installation, and can be useful when running an ASP.NET application from the REPL. Example frameworks are:
    • Microsoft.NETCore.App (default)
    • Microsoft.AspNetCore.All
    • Microsoft.AspNetCore.App
    • Microsoft.WindowsDesktop.App
  • -t <theme.json> or --theme <theme.json>: Read a theme file for syntax highlighting. This theme file associates C# syntax classifications with colors. The color values can be full RGB, or ANSI color names (defined in your terminal's theme). The NO_COLOR standard is supported.
  • --trace: Produce a trace file in the current directory that logs CSharpRepl internals. Useful for CSharpRepl bug reports.
  • -v or --version: Show version number and exit.
  • -h or --help: Show help and exit.
• response-file.rsp: A filepath of an .rsp file, containing any of the above command line options.
• script-file.csx: A filepath of a .csx file, containing lines of C# to evaluate before starting the REPL. Arguments to this script can be passed as <additional-arguments>, after a double hyphen (--), and will be available in a global args variable.

If you have dotnet-suggest enabled, all options can be tab-completed, including values provided to --framework and .NET namespaces provided to --using.

Integrating with other software

C# REPL is a standalone software application, but it can be useful to integrate it with other developer tools:

Windows Terminal

To add C# REPL as a menu entry in Windows Terminal, add the following profile to Windows Terminal's settings.json configuration file (under the JSON property profiles.list):

{
    "name": "C# REPL",
    "commandline": "csharprepl"
},

To get the exact colors shown in the screenshots in this README, install the Windows Terminal Dracula theme.

Visual Studio Code

To use the C# REPL with Visual Studio Code, simply run the csharprepl command in the Visual Studio Code terminal. To send commands to the REPL, use the built-in Terminal: Run Selected Text In Active Terminal command from the Command Palette (workbench.action.terminal.runSelectedText).

Windows OS

To add the C# REPL to the Windows Start Menu for quick access, you can run the following PowerShell command, which will start C# REPL in Windows Terminal:

$shell = New-Object -ComObject WScript.Shell
$shortcut = $shell.CreateShortcut("$env:appdata\Microsoft\Windows\Start Menu\Programs\csharprepl.lnk")
$shortcut.TargetPath = "wt.exe"
$shortcut.Arguments = "-w 0 nt csharprepl.exe"
$shortcut.Save()

You may also wish to add a shorter alias for C# REPL, which can be done by creating a .cmd file somewhere on your path. For example, put the following contents in C:\Users\username\.dotnet\tools\csr.cmd:

wt -w 0 nt csharprepl

This will allow you to launch C# REPL by running csr from anywhere that accepts Windows commands, like the Window Run dialog.

Comparison with other REPLs

This project is far from being the first REPL for C#. Here are some other projects; if this project doesn't suit you, another one might!

Visual Studio's C# Interactive pane is full-featured (it has syntax highlighting and intellisense) and is part of Visual Studio. This deep integration with Visual Studio is both a benefit from a workflow perspective, and a drawback as it's not cross-platform. As far as I know, the C# Interactive pane does not support NuGet packages or navigating to documentation/source code. Subjectively, it does not follow typical command line keybindings, so can feel a bit foreign.

csi.exe ships with C# and is a command line REPL. It's great because it's a cross platform REPL that comes out of the box, but it doesn't support syntax highlighting or autocompletion.

dotnet script allows you to run C# scripts from the command line. It has a REPL built-in, but the predominant focus seems to be as a script runner. It's a great tool, though, and has a strong community following.

dotnet interactive is a tool from Microsoft that creates a Jupyter notebook for C#, runnable through Visual Studio Code. It also provides a general framework useful for running REPLs.

Download Details:
Author: waf
Source Code: https://github.com/waf/CSharpRepl
License: MPL-2.0 License

#dotnet  #aspdotnet  #csharp 

NBB: Ad-hoc CLJS Scripting on Node.js

Nbb

Not babashka. Node.js babashka!?

Ad-hoc CLJS scripting on Node.js.

Status

Experimental. Please report issues here.

Goals and features

Nbb's main goal is to make it easy to get started with ad hoc CLJS scripting on Node.js.

Additional goals and features are:

• Fast startup without relying on a custom version of Node.js.
• Small artifact (current size is around 1.2MB).
• First class macros.
• Support building small TUI apps using Reagent.
• Complement babashka with libraries from the Node.js ecosystem.

Requirements

Nbb requires Node.js v12 or newer.

How does this tool work?

CLJS code is evaluated through SCI, the same interpreter that powers babashka. Because SCI works with advanced compilation, the bundle size, especially when combined with other dependencies, is smaller than what you get with self-hosted CLJS. That makes startup faster. The trade-off is that execution is less performant and that only a subset of CLJS is available (e.g. no deftype, yet).

Usage

Install nbb from NPM:

$ npm install nbb -g

Omit -g for a local install.

Try out an expression:

$ nbb -e '(+ 1 2 3)'
6

And then install some other NPM libraries to use in the script. E.g.:

$ npm install csv-parse shelljs zx

Create a script which uses the NPM libraries:

(ns script
  (:require ["csv-parse/lib/sync$default" :as csv-parse]
            ["fs" :as fs]
            ["path" :as path]
            ["shelljs$default" :as sh]
            ["term-size$default" :as term-size]
            ["zx$default" :as zx]
            ["zx$fs" :as zxfs]
            [nbb.core :refer [*file*]]))

(prn (path/resolve "."))

(prn (term-size))

(println (count (str (fs/readFileSync *file*))))

(prn (sh/ls "."))

(prn (csv-parse "foo,bar"))

(prn (zxfs/existsSync *file*))

(zx/$ #js ["ls"])

Call the script:

$ nbb script.cljs
"/private/tmp/test-script"
#js {:columns 216, :rows 47}
510
#js ["node_modules" "package-lock.json" "package.json" "script.cljs"]
#js [#js ["foo" "bar"]]
true
$ ls
node_modules
package-lock.json
package.json
script.cljs

Macros

Nbb has first class support for macros: you can define them right inside your .cljs file, like you are used to from JVM Clojure. Consider the plet macro to make working with promises more palatable:

(defmacro plet
  [bindings & body]
  (let [binding-pairs (reverse (partition 2 bindings))
        body (cons 'do body)]
    (reduce (fn [body [sym expr]]
              (let [expr (list '.resolve 'js/Promise expr)]
                (list '.then expr (list 'clojure.core/fn (vector sym)
                                        body))))
            body
            binding-pairs)))

Using this macro we can look async code more like sync code. Consider this puppeteer example:

(-> (.launch puppeteer)
      (.then (fn [browser]
               (-> (.newPage browser)
                   (.then (fn [page]
                            (-> (.goto page "https://clojure.org")
                                (.then #(.screenshot page #js{:path "screenshot.png"}))
                                (.catch #(js/console.log %))
                                (.then #(.close browser)))))))))

Using plet this becomes:

(plet [browser (.launch puppeteer)
       page (.newPage browser)
       _ (.goto page "https://clojure.org")
       _ (-> (.screenshot page #js{:path "screenshot.png"})
             (.catch #(js/console.log %)))]
      (.close browser))

See the puppeteer example for the full code.

Since v0.0.36, nbb includes promesa which is a library to deal with promises. The above plet macro is similar to promesa.core/let.

Startup time

$ time nbb -e '(+ 1 2 3)'
6
nbb -e '(+ 1 2 3)'   0.17s  user 0.02s system 109% cpu 0.168 total

The baseline startup time for a script is about 170ms seconds on my laptop. When invoked via npx this adds another 300ms or so, so for faster startup, either use a globally installed nbb or use $(npm bin)/nbb script.cljs to bypass npx.

Dependencies

NPM dependencies

Nbb does not depend on any NPM dependencies. All NPM libraries loaded by a script are resolved relative to that script. When using the Reagent module, React is resolved in the same way as any other NPM library.

Classpath

To load .cljs files from local paths or dependencies, you can use the --classpath argument. The current dir is added to the classpath automatically. So if there is a file foo/bar.cljs relative to your current dir, then you can load it via (:require [foo.bar :as fb]). Note that nbb uses the same naming conventions for namespaces and directories as other Clojure tools: foo-bar in the namespace name becomes foo_bar in the directory name.

To load dependencies from the Clojure ecosystem, you can use the Clojure CLI or babashka to download them and produce a classpath:

$ classpath="$(clojure -A:nbb -Spath -Sdeps '{:aliases {:nbb {:replace-deps {com.github.seancorfield/honeysql {:git/tag "v2.0.0-rc5" :git/sha "01c3a55"}}}}}')"

and then feed it to the --classpath argument:

$ nbb --classpath "$classpath" -e "(require '[honey.sql :as sql]) (sql/format {:select :foo :from :bar :where [:= :baz 2]})"
["SELECT foo FROM bar WHERE baz = ?" 2]

Currently nbb only reads from directories, not jar files, so you are encouraged to use git libs. Support for .jar files will be added later.

Current file

The name of the file that is currently being executed is available via nbb.core/*file* or on the metadata of vars:

(ns foo
  (:require [nbb.core :refer [*file*]]))

(prn *file*) ;; "/private/tmp/foo.cljs"

(defn f [])
(prn (:file (meta #'f))) ;; "/private/tmp/foo.cljs"

Reagent

Nbb includes reagent.core which will be lazily loaded when required. You can use this together with ink to create a TUI application:

$ npm install ink

ink-demo.cljs:

(ns ink-demo
  (:require ["ink" :refer [render Text]]
            [reagent.core :as r]))

(defonce state (r/atom 0))

(doseq [n (range 1 11)]
  (js/setTimeout #(swap! state inc) (* n 500)))

(defn hello []
  [:> Text {:color "green"} "Hello, world! " @state])

(render (r/as-element [hello]))

Promesa

Working with callbacks and promises can become tedious. Since nbb v0.0.36 the promesa.core namespace is included with the let and do! macros. An example:

(ns prom
  (:require [promesa.core :as p]))

(defn sleep [ms]
  (js/Promise.
   (fn [resolve _]
     (js/setTimeout resolve ms))))

(defn do-stuff
  []
  (p/do!
   (println "Doing stuff which takes a while")
   (sleep 1000)
   1))

(p/let [a (do-stuff)
        b (inc a)
        c (do-stuff)
        d (+ b c)]
  (prn d))

$ nbb prom.cljs
Doing stuff which takes a while
Doing stuff which takes a while
3

Also see API docs.

Js-interop

Since nbb v0.0.75 applied-science/js-interop is available:

(ns example
  (:require [applied-science.js-interop :as j]))

(def o (j/lit {:a 1 :b 2 :c {:d 1}}))

(prn (j/select-keys o [:a :b])) ;; #js {:a 1, :b 2}
(prn (j/get-in o [:c :d])) ;; 1

Most of this library is supported in nbb, except the following:

• destructuring using :syms
• property access using .-x notation. In nbb, you must use keywords.

See the example of what is currently supported.

Examples

See the examples directory for small examples.

Also check out these projects built with nbb:

• c64core: retrocompute aesthetics twitter bot
• gallery.cljs: script to download walpapers from windowsonearth.org.
• nbb-action-example: example of a Github action built with nbb.

API

See API documentation.

Migrating to shadow-cljs

See this gist on how to convert an nbb script or project to shadow-cljs.

Build

Prequisites:

• babashka >= 0.4.0
• Clojure CLI >= 1.10.3.933
• Node.js 16.5.0 (lower version may work, but this is the one I used to build)

To build:

• Clone and cd into this repo
• bb release

Run bb tasks for more project-related tasks.

Download Details:
Author: borkdude
Download Link: Download The Source Code
Official Website: https://github.com/borkdude/nbb 
License: EPL-1.0

#node #javascript

Dotnet Script: Run C# Scripts From The .NET CLI

dotnet script

Run C# scripts from the .NET CLI, define NuGet packages inline and edit/debug them in VS Code - all of that with full language services support from OmniSharp.

NuGet Packages

Name	Version	Framework(s)
dotnet-script (global tool)		net6.0, net5.0, netcoreapp3.1
Dotnet.Script (CLI as Nuget)		net6.0, net5.0, netcoreapp3.1
Dotnet.Script.Core		netcoreapp3.1 , netstandard2.0
Dotnet.Script.DependencyModel		netstandard2.0
Dotnet.Script.DependencyModel.Nuget		netstandard2.0

Installing

Prerequisites

The only thing we need to install is .NET Core 3.1 or .NET 5.0 SDK.

.NET Core Global Tool

.NET Core 2.1 introduced the concept of global tools meaning that you can install dotnet-script using nothing but the .NET CLI.

dotnet tool install -g dotnet-script

You can invoke the tool using the following command: dotnet-script
Tool 'dotnet-script' (version '0.22.0') was successfully installed.

The advantage of this approach is that you can use the same command for installation across all platforms. .NET Core SDK also supports viewing a list of installed tools and their uninstallation.

dotnet tool list -g

Package Id         Version      Commands
---------------------------------------------
dotnet-script      0.22.0       dotnet-script

dotnet tool uninstall dotnet-script -g

Tool 'dotnet-script' (version '0.22.0') was successfully uninstalled.

Windows

choco install dotnet.script

We also provide a PowerShell script for installation.

(new-object Net.WebClient).DownloadString("https://raw.githubusercontent.com/filipw/dotnet-script/master/install/install.ps1") | iex

Linux and Mac

curl -s https://raw.githubusercontent.com/filipw/dotnet-script/master/install/install.sh | bash

If permission is denied we can try with sudo

curl -s https://raw.githubusercontent.com/filipw/dotnet-script/master/install/install.sh | sudo bash

Docker

A Dockerfile for running dotnet-script in a Linux container is available. Build:

cd build
docker build -t dotnet-script -f Dockerfile ..

And run:

docker run -it dotnet-script --version

Github

You can manually download all the releases in zip format from the GitHub releases page.

Usage

Our typical helloworld.csx might look like this:

Console.WriteLine("Hello world!");

That is all it takes and we can execute the script. Args are accessible via the global Args array.

dotnet script helloworld.csx

Scaffolding

Simply create a folder somewhere on your system and issue the following command.

dotnet script init

This will create main.csx along with the launch configuration needed to debug the script in VS Code.

.
├── .vscode
│   └── launch.json
├── main.csx
└── omnisharp.json

We can also initialize a folder using a custom filename.

dotnet script init custom.csx

Instead of main.csx which is the default, we now have a file named custom.csx.

.
├── .vscode
│   └── launch.json
├── custom.csx
└── omnisharp.json

Note: Executing dotnet script init inside a folder that already contains one or more script files will not create the main.csx file.

Running scripts

Scripts can be executed directly from the shell as if they were executables.

foo.csx arg1 arg2 arg3

OSX/Linux

Just like all scripts, on OSX/Linux you need to have a #! and mark the file as executable via chmod +x foo.csx. If you use dotnet script init to create your csx it will automatically have the #! directive and be marked as executable.

The OSX/Linux shebang directive should be #!/usr/bin/env dotnet-script

#!/usr/bin/env dotnet-script
Console.WriteLine("Hello world");

You can execute your script using dotnet script or dotnet-script, which allows you to pass arguments to control your script execution more.

foo.csx arg1 arg2 arg3
dotnet script foo.csx -- arg1 arg2 arg3
dotnet-script foo.csx -- arg1 arg2 arg3

Passing arguments to scripts

All arguments after -- are passed to the script in the following way:

dotnet script foo.csx -- arg1 arg2 arg3

Then you can access the arguments in the script context using the global Args collection:

foreach (var arg in Args)
{
    Console.WriteLine(arg);
}

All arguments before -- are processed by dotnet script. For example, the following command-line

dotnet script -d foo.csx -- -d

will pass the -d before -- to dotnet script and enable the debug mode whereas the -d after -- is passed to script for its own interpretation of the argument.

NuGet Packages

dotnet script has built-in support for referencing NuGet packages directly from within the script.

#r "nuget: AutoMapper, 6.1.0"

Note: Omnisharp needs to be restarted after adding a new package reference

Package Sources

We can define package sources using a NuGet.Config file in the script root folder. In addition to being used during execution of the script, it will also be used by OmniSharp that provides language services for packages resolved from these package sources.

As an alternative to maintaining a local NuGet.Config file we can define these package sources globally either at the user level or at the computer level as described in Configuring NuGet Behaviour

It is also possible to specify packages sources when executing the script.

dotnet script foo.csx -s https://SomePackageSource

Multiple packages sources can be specified like this:

dotnet script foo.csx -s https://SomePackageSource -s https://AnotherPackageSource

Creating DLLs or Exes from a CSX file

Dotnet-Script can create a standalone executable or DLL for your script.

Switch	Long switch	description
-o	--output	Directory where the published executable should be placed. Defaults to a 'publish' folder in the current directory.
-n	--name	The name for the generated DLL (executable not supported at this time). Defaults to the name of the script.
	--dll	Publish to a .dll instead of an executable.
-c	--configuration	Configuration to use for publishing the script [Release/Debug]. Default is "Debug"
-d	--debug	Enables debug output.
-r	--runtime	The runtime used when publishing the self contained executable. Defaults to your current runtime.

The executable you can run directly independent of dotnet install, while the DLL can be run using the dotnet CLI like this:

dotnet script exec {path_to_dll} -- arg1 arg2

Caching

We provide two types of caching, the dependency cache and the execution cache which is explained in detail below. In order for any of these caches to be enabled, it is required that all NuGet package references are specified using an exact version number. The reason for this constraint is that we need to make sure that we don't execute a script with a stale dependency graph.

Dependency Cache

In order to resolve the dependencies for a script, a dotnet restore is executed under the hood to produce a project.assets.json file from which we can figure out all the dependencies we need to add to the compilation. This is an out-of-process operation and represents a significant overhead to the script execution. So this cache works by looking at all the dependencies specified in the script(s) either in the form of NuGet package references or assembly file references. If these dependencies matches the dependencies from the last script execution, we skip the restore and read the dependencies from the already generated project.assets.json file. If any of the dependencies has changed, we must restore again to obtain the new dependency graph.

Execution cache

In order to execute a script it needs to be compiled first and since that is a CPU and time consuming operation, we make sure that we only compile when the source code has changed. This works by creating a SHA256 hash from all the script files involved in the execution. This hash is written to a temporary location along with the DLL that represents the result of the script compilation. When a script is executed the hash is computed and compared with the hash from the previous compilation. If they match there is no need to recompile and we run from the already compiled DLL. If the hashes don't match, the cache is invalidated and we recompile.

You can override this automatic caching by passing --no-cache flag, which will bypass both caches and cause dependency resolution and script compilation to happen every time we execute the script.

Cache Location

The temporary location used for caches is a sub-directory named dotnet-script under (in order of priority):

1. The path specified for the value of the environment variable named DOTNET_SCRIPT_CACHE_LOCATION, if defined and value is not empty.
2. Linux distributions only: $XDG_CACHE_HOME if defined otherwise $HOME/.cache
3. macOS only: ~/Library/Caches
4. The value returned by Path.GetTempPath for the platform.

 

Debugging

The days of debugging scripts using Console.WriteLine are over. One major feature of dotnet script is the ability to debug scripts directly in VS Code. Just set a breakpoint anywhere in your script file(s) and hit F5(start debugging)

Script Packages

Script packages are a way of organizing reusable scripts into NuGet packages that can be consumed by other scripts. This means that we now can leverage scripting infrastructure without the need for any kind of bootstrapping.

Creating a script package

A script package is just a regular NuGet package that contains script files inside the content or contentFiles folder.

The following example shows how the scripts are laid out inside the NuGet package according to the standard convention .

└── contentFiles
    └── csx
        └── netstandard2.0
            └── main.csx

This example contains just the main.csx file in the root folder, but packages may have multiple script files either in the root folder or in subfolders below the root folder.

When loading a script package we will look for an entry point script to be loaded. This entry point script is identified by one of the following.

• A script called main.csx in the root folder
• A single script file in the root folder

If the entry point script cannot be determined, we will simply load all the scripts files in the package.

The advantage with using an entry point script is that we can control loading other scripts from the package.

Consuming a script package

To consume a script package all we need to do specify the NuGet package in the #loaddirective.

The following example loads the simple-targets package that contains script files to be included in our script.

#load "nuget:simple-targets-csx, 6.0.0"

using static SimpleTargets;
var targets = new TargetDictionary();

targets.Add("default", () => Console.WriteLine("Hello, world!"));

Run(Args, targets);

Note: Debugging also works for script packages so that we can easily step into the scripts that are brought in using the #load directive.

Remote Scripts

Scripts don't actually have to exist locally on the machine. We can also execute scripts that are made available on an http(s) endpoint.

This means that we can create a Gist on Github and execute it just by providing the URL to the Gist.

This Gist contains a script that prints out "Hello World"

We can execute the script like this

dotnet script https://gist.githubusercontent.com/seesharper/5d6859509ea8364a1fdf66bbf5b7923d/raw/0a32bac2c3ea807f9379a38e251d93e39c8131cb/HelloWorld.csx

That is a pretty long URL, so why don't make it a TinyURL like this:

dotnet script https://tinyurl.com/y8cda9zt

Script Location

A pretty common scenario is that we have logic that is relative to the script path. We don't want to require the user to be in a certain directory for these paths to resolve correctly so here is how to provide the script path and the script folder regardless of the current working directory.

public static string GetScriptPath([CallerFilePath] string path = null) => path;
public static string GetScriptFolder([CallerFilePath] string path = null) => Path.GetDirectoryName(path);

Tip: Put these methods as top level methods in a separate script file and #load that file wherever access to the script path and/or folder is needed.

REPL

This release contains a C# REPL (Read-Evaluate-Print-Loop). The REPL mode ("interactive mode") is started by executing dotnet-script without any arguments.

The interactive mode allows you to supply individual C# code blocks and have them executed as soon as you press Enter. The REPL is configured with the same default set of assembly references and using statements as regular CSX script execution.

Basic usage

Once dotnet-script starts you will see a prompt for input. You can start typing C# code there.

~$ dotnet script
> var x = 1;
> x+x
2

If you submit an unterminated expression into the REPL (no ; at the end), it will be evaluated and the result will be serialized using a formatter and printed in the output. This is a bit more interesting than just calling ToString() on the object, because it attempts to capture the actual structure of the object. For example:

~$ dotnet script
> var x = new List<string>();
> x.Add("foo");
> x
List<string>(1) { "foo" }
> x.Add("bar");
> x
List<string>(2) { "foo", "bar" }
>

Inline Nuget packages

REPL also supports inline Nuget packages - meaning the Nuget packages can be installed into the REPL from within the REPL. This is done via our #r and #load from Nuget support and uses identical syntax.

~$ dotnet script
> #r "nuget: Automapper, 6.1.1"
> using AutoMapper;
> typeof(MapperConfiguration)
[AutoMapper.MapperConfiguration]
> #load "nuget: simple-targets-csx, 6.0.0";
> using static SimpleTargets;
> typeof(TargetDictionary)
[Submission#0+SimpleTargets+TargetDictionary]

Multiline mode

Using Roslyn syntax parsing, we also support multiline REPL mode. This means that if you have an uncompleted code block and press Enter, we will automatically enter the multiline mode. The mode is indicated by the * character. This is particularly useful for declaring classes and other more complex constructs.

~$ dotnet script
> class Foo {
* public string Bar {get; set;}
* }
> var foo = new Foo();

REPL commands

Aside from the regular C# script code, you can invoke the following commands (directives) from within the REPL:

Command	Description
#load	Load a script into the REPL (same as #load usage in CSX)
#r	Load an assembly into the REPL (same as #r usage in CSX)
#reset	Reset the REPL back to initial state (without restarting it)
#cls	Clear the console screen without resetting the REPL state
#exit	Exits the REPL

Seeding REPL with a script

You can execute a CSX script and, at the end of it, drop yourself into the context of the REPL. This way, the REPL becomes "seeded" with your code - all the classes, methods or variables are available in the REPL context. This is achieved by running a script with an -i flag.

For example, given the following CSX script:

var msg = "Hello World";
Console.WriteLine(msg);

When you run this with the -i flag, Hello World is printed, REPL starts and msg variable is available in the REPL context.

~$ dotnet script foo.csx -i
Hello World
>

You can also seed the REPL from inside the REPL - at any point - by invoking a #load directive pointed at a specific file. For example:

~$ dotnet script
> #load "foo.csx"
Hello World
>

Piping

The following example shows how we can pipe data in and out of a script.

The UpperCase.csx script simply converts the standard input to upper case and writes it back out to standard output.

using (var streamReader = new StreamReader(Console.OpenStandardInput()))
{
    Write(streamReader.ReadToEnd().ToUpper());
}

We can now simply pipe the output from one command into our script like this.

echo "This is some text" | dotnet script UpperCase.csx
THIS IS SOME TEXT

Debugging

The first thing we need to do add the following to the launch.config file that allows VS Code to debug a running process.

{
    "name": ".NET Core Attach",
    "type": "coreclr",
    "request": "attach",
    "processId": "${command:pickProcess}"
}

To debug this script we need a way to attach the debugger in VS Code and the simplest thing we can do here is to wait for the debugger to attach by adding this method somewhere.

public static void WaitForDebugger()
{
    Console.WriteLine("Attach Debugger (VS Code)");
    while(!Debugger.IsAttached)
    {
    }
}

To debug the script when executing it from the command line we can do something like

WaitForDebugger();
using (var streamReader = new StreamReader(Console.OpenStandardInput()))
{
    Write(streamReader.ReadToEnd().ToUpper()); // <- SET BREAKPOINT HERE
}

Now when we run the script from the command line we will get

$ echo "This is some text" | dotnet script UpperCase.csx
Attach Debugger (VS Code)

This now gives us a chance to attach the debugger before stepping into the script and from VS Code, select the .NET Core Attach debugger and pick the process that represents the executing script.

Once that is done we should see our breakpoint being hit.

Configuration(Debug/Release)

By default, scripts will be compiled using the debug configuration. This is to ensure that we can debug a script in VS Code as well as attaching a debugger for long running scripts.

There are however situations where we might need to execute a script that is compiled with the release configuration. For instance, running benchmarks using BenchmarkDotNet is not possible unless the script is compiled with the release configuration.

We can specify this when executing the script.

dotnet script foo.csx -c release

 

Nullable reference types

Starting from version 0.50.0, dotnet-script supports .Net Core 3.0 and all the C# 8 features. The way we deal with nullable references types in dotnet-script is that we turn every warning related to nullable reference types into compiler errors. This means every warning between CS8600 and CS8655 are treated as an error when compiling the script.

Nullable references types are turned off by default and the way we enable it is using the #nullable enable compiler directive. This means that existing scripts will continue to work, but we can now opt-in on this new feature.

#!/usr/bin/env dotnet-script

#nullable enable

string name = null;

Trying to execute the script will result in the following error

main.csx(5,15): error CS8625: Cannot convert null literal to non-nullable reference type.

We will also see this when working with scripts in VS Code under the problems panel.

Download Details:
Author: filipw
Source Code: https://github.com/filipw/dotnet-script
License: MIT License

#dotnet  #aspdotnet  #csharp 

Htmlwidgets Binding R Commands to The BioCircos.js Library

BioCircos.R

Simple htmlwidgets binding R commands to the BioCircos.js library

---

Introduction

This package allows to implement in 'R' Circos-like visualizations of genomic data, as proposed by the BioCircos.js JavaScript library, based on the JQuery and D3 technologies.
For a complete list of all the parameters available, please refer to the package documentation.

Motivation

The amount of data produced nowadays in a lot of different fields assesses the relevance of reactive analyses and interactive display of the results. This is especially true in biology, where the cost of sequencing data has dropped must faster than the Moore's law prediction. New ways of integrating different levels of information and accelerating the interpretation are therefore needed.

The integration challenge appears to be of major importance, as it allows a deeper understanding of the biological phenomena happening, that cannot be observed in the single analyses independently.

This package aims at offering an easy way of producing Circos-like visualizations to face distinct challenges :

• On the one hand, data integration and visualization: Circos is a popular tool to combine different biological information on a single plot.
• On the other hand, reactivity and interactivity: thanks to the htmlwidgets framework, the figures produced by this package are responsive to mouse events and display useful tooltips, and they can be integrated in shiny apps. Once the analyses have been performed and the shiny app coded, it is possible for the end-user to explore a massive amount of biological data without any programming or bioinformatics knowledge.

The terminology used here arises from genomics but this tool may be of interest for different situations where different positional or temporal informations must be combined.

Installation

To install this package, you can use CRAN (the central R package repository) to get the last stable release or build the last development version directly from the GitHub repository.

From CRAN

install.packages('BioCircos')

From Github

# You need devtools for that
if (!require('devtools')){install.packages('devtools')}
devtools::install_github('lvulliard/BioCircos.R', build_vignettes = TRUE))

Compatibility and troubleshooting

Since the visualizations are powered by JavaScript, they are affected by the environment in which they are displayed.

• If nothing shows up in the Rstudio viewer pane, try displaying the plot you generated in your browser instead. You can export the figure using the Save as Web Page... option in the Export tab of the viewer pane.
• If nothing shows up in a shiny application or an Rmarkdown document, try to update your web browser. See the vignettes for examples of BioCircos plots that should be correctly displayed.
• Rotation of labels using the genomeLabelOrientation parameter leads to a slight offset of the text when displayed in Firefox because some recent CSS options are not yet implemented.

Obseved behavior

• Firefox 55, Chrome 54 and later versions work as expected.
• Firefox 46, Chrome 53 and past versions do not display the plots at all.
• Firefox 47 to 54 do not include all features, such as zooming.

Tutorial

See the vignettes to learn how to use BioCircos visualizations.

vignette('BioCircos')

Original work

BioCircos.js : an Interactive Circos JavaScript Library for Biological Data Visualization on Web Applications.

https://github.com/YaCui/Biocircos.js

http://bioinfo.ibp.ac.cn/biocircos/

http://www.ncbi.nlm.nih.gov/pubmed/26819473

Documentation: http://bioinfo.ibp.ac.cn/biocircos/document/index.html

Modifications

The following features have been added to the original BioCircos.js library, based on version 1.1.2:

• Parameter snp_value_maxmin_instance set by SNPsettings.range when provided, to allow the use of a pre-defined range of values for the SNP track.
• Similar parameters added for the range of Histogram/Bar tracks, Line tracks, CNV tracks and Heatmap tracks (for the range to be used for color mapping).
• Parameter opacity added to each elements of SNP and Arc tracks.
• Changes were made in order to allow rotation of genome labels with the new parameter genomeLabelOrientation and the radial offset dy is now directly integrated in the label translation.

Contact

To report bugs, request features or for any question or remark regarding this package, please use the GitHub page or contact Loan Vulliard.

Credits

The creation and implementation of the BioCircos.js JavaScript library is an independent work attributed to Ya Cui and Xiaowei Chen.
This work is described in the following scientific article: BioCircos.js: an Interactive Circos JavaScript Library for Biological Data Visualization on Web Applications. Cui, Y., et al. Bioinformatics. (2016).

This package relies on several open source projects other R packages, and is made possible thanks to shiny and htmlwidgets.

The package heatmaply was used as a model for this vignette, as well as for the htmlwidgets configuration.

Download Details:

Author: lvulliard
Source Code: https://github.com/lvulliard/BioCircos.R 
License:  GPL-2.0 license

#r #shiny 

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