Architect – Getting Started

Documentation: Installation

Mon, 01 Jan 0001 00:00:00 +0000

The latest versions of Architect are available on our downloads page. Architect is available for Windows, Mac and Linux.

Windows

Stable release

On the download site, click on the “Architect for 64-bit Windows” link. Your download will start automatically.

Once the download is complete, click on the .exe file to start installation.

If asked “Do you want to allow the following program from an unknown publisher to make changes to this computer?”, click Yes.

The Architect Setup Wizard will then launch.

Click Next. On the following screen, choose the folder where you would like to install Architect.

Click Install, and installation will proceed automatically. Once installation has concluded, click Finish to close the installer.

Snapshot release

Snapshot releases for Windows are made available on our Nexus repository. The installation procedure is identical as for the stable release.

Mac

Stable release

On the download site, click on the Architect for Mac OS X link. Your download will start automatically.

Once the download is complete, click on the .pkg file to start installation.

Control-click the Architect app icon, then choose Open from the shortcut menu.

If a popup with “architect 1.0.0.pkg” cannot be opened because it is from an unidentified developer.", then just click ok and try opening the .pkg file again.

After a couple tries the next popup will appear “macOS cannot verify the developer of architect 1.0.0.pkg. Are you sure you want to open it?”. When this popup appears just click “Open”.

After clicking “Open” just follow the installation wizard until the message “The installation was successful” appears.

During the actual installation step you might be asked to provide you password or to you use the “Touch ID” (if available) to finish the “Architect” installation.

After the installation has successfully finished, close the wizard and the “Architect” application will be available in you “Applications” folder.

Snapshot release

Snapshot releases for Mac are made available on our Nexus repository. The installation procedure is identical as for the stable release.

Linux

Installation from repositories

The easiest way to install Architect on Ubuntu is to use our package repository. Follow the instructions for your version of Ubuntu.

Bionic (Ubuntu 18.04)

Stable release

sudo apt update
sudo apt install gpg apt-transport-https ca-certificates wget software-properties-common
wget -qO - https://getarchitect.io/repo-key.gpg | sudo apt-key add -
sudo add-apt-repository 'deb [arch=amd64] https://apt.getarchitect.io/bionic/ bionic main'
sudo apt install architect

Snapshot release

Note: this repository provides development versions of Architect, use with care.

sudo apt update
sudo apt install gpg apt-transport-https ca-certificates wget software-properties-common
wget -qO - https://getarchitect.io/repo-key.gpg | sudo apt-key add -
sudo add-apt-repository 'deb [arch=amd64] https://apt.getarchitect.io/bionic-snapshot/ bionic main'
sudo apt install architect

Focal (Ubuntu 20.04)

Stable release

sudo apt update
sudo apt install gpg apt-transport-https ca-certificates wget software-properties-common
wget -qO - https://getarchitect.io/repo-key.gpg | sudo apt-key add -
sudo add-apt-repository 'deb [arch=amd64] https://apt.getarchitect.io/focal/ focal main'
sudo apt install architect

Snapshot release

Note: this repository provides development versions of Architect, use with care.

sudo apt update
sudo apt install gpg apt-transport-https ca-certificates wget software-properties-common
wget -qO - https://getarchitect.io/repo-key.gpg | sudo apt-key add -
sudo add-apt-repository 'deb [arch=amd64] https://apt.getarchitect.io/focal-snapshot/ focal main'
sudo apt install architect

Jammy (Ubuntu 22.04)

Stable release

sudo apt update
sudo apt install gpg apt-transport-https ca-certificates wget software-properties-common
wget -qO - https://getarchitect.io/repo-key.gpg | sudo apt-key add -
sudo add-apt-repository 'deb [arch=amd64] https://apt.getarchitect.io/jammy/ jammy main'
sudo apt install architect

Snapshot release

Note: this repository provides development versions of Architect, use with care.

sudo apt update
sudo apt install gpg apt-transport-https ca-certificates wget software-properties-common
wget -qO - https://getarchitect.io/repo-key.gpg | sudo apt-key add -
sudo add-apt-repository 'deb [arch=amd64] https://apt.getarchitect.io/jammy-snapshot/ jammy main'
sudo apt install architect

Manual installation

Alternatively, .deb and .rpm package files are available for Architect on our downloads page.

Ubuntu

Download the .deb file, then type in the terminal:

dpkg -i XXX.deb

where ‘XXX.deb’ is the name of the downloaded .deb file.

You can also double-click the .deb file to open Ubuntu Software Center. Click Install and enter your password if prompted:

CentOS

Download the .rpm file, then type in the terminal:

rpm -i XXX.rpm

where ‘XXX.rpm’ is the name of the downloaded .rpm file.

Documentation: Your First Project

Mon, 01 Jan 0001 00:00:00 +0000

Your first look at Architect is a fairly blank canvas.

For the uninitiated, this can seem a little disorienting. We’ll walk you through the steps of getting your first project up and running.

Using Project Explorer to Create a Project

The Project Explorer is the directory of all your defined Architect projects. Projects are home to various files, and most commonly will contain things like folders, R scripts and data files.

To create a new project, simply right-click inside the Project Explorer and select New > Project. This may also be done via the main menu with File > New > Project.

Architect can be used to develop projects in various programming languages. To create an R project, use the settings below.

By default, a new project will be created inside of your workspace (in Windows, this is a directory like C:/Users/Username/.architect/workspace). It’s easy, however, to override this default and link to existing directories on your computer.

Projects in Other Directories

To create a project that points to an existing directory, uncheck the Use default location box and click Browse to navigate to the desired folder. This is particularly useful for projects based on a git repository.

For now, we’ll use the default location, name our first project and click Finish.

Scripts and the Console

We’ll now populate our first project. Create an R script in a given folder by right-clicking the folder and selecting New > R Script File. You may also paste files from your clipboard.

Launching a Console in a Directory

R code is run in a view called the Console. An R console launches automatically when you open Architect.

We cover the functionaly of these many buttons in a later section, but for now we direct our attention to the top-right corner. The console lists our current working directory as ‘C:\Program Files\Architect_0.9.1’, but you’ll likely want your code to be evaluated elsewhere. Although you can change the working directory with a setwd() call, often it’s easiest to select a folder from the Project Explorer and launch a fresh R Console from there.

To do so, simply click on the desired folder, then click the green ‘play’ button in the top toolbar.

This launches a fresh console in the selected directory.

Running Code in the Console

With a console open in our ‘myFirstProject’ directory, we’re ready to run a basic script.

head(cars)

dir.create("data")
?write.csv
write.csv(file = "./data/carsData.csv", cars)

plot(cars$speed, cars$dist)

There are several ways to run code within Architect. Most commonly, users use customizable keyboard shortcuts. By default, the command Ctrl+R, Ctrl+R will fun a selection of code in the console. A list of commonly used default keyboard shortcuts are given in the Architect Reference Card. To customize these inputs, please refer to the section Customizing Keyboard Shortcuts.

Alternatively, it is possible to simply copy and paste a selection of R code directly into the console. Highlighting and right-clicking code in a script also presents options for evaluating code.

After running the above section of code, your Architect session will look something like this:

We’ll notice that as certain lines of code were evaluated, Architect automatically opened relevant views. The above code prompted the opening of the R Help and R Graphics views. This is very useful, but we immediately see some issues. The R Help view is quite small, our graph isn’t properly scaled to the window, and at the moment, we don’t even need the Outline view.

In the next section, we’ll cover how to fully customize your Architect layout, and save presets so you can easily switch between your configurations (especially useful when switching from a single monitor to dual monitor setup).

Documentation: The Interface

Mon, 01 Jan 0001 00:00:00 +0000

Customizing View and Saving Perspectives

Customizing Architect’s interface is easy. This section presents several ways to configure the layout to your liking.

Dragging Borders

Windows within Architect can be resized by clicking on the grey borders between views and dragging them to the desired location.

Rearranging Views

To split or merge different views, click, drag and drop! An existing window can be further split horizontally or vertically.

Popping Out Views

Views can also be popped out of Architect entirely. This is particularly useful when customizing for a dual-monitor setup.

Minimizing and Maximizing

Groups of views can be minimized and maximized with single clicks. Below, we minimize the Object Browser and R Help views. A side pane for these minimized views is then created on the left-hand side.

Saving and Switching Perspectives

Once you’ve customized the layout to your liking, you can save your layout as a ‘Perspective’. In this way, you can quickly switch between your custom perspectives, depending on the type of work you’re doing or how many monitors you have on hand.

Project Explorer

The number of projects you have can grow quite large, and Architect provides tools to help you manage the chaos.

Linking Scripts and Project Explorer

To help avoid excessive scrolling through the Project Explorer, or confusion over similarly named files, Architect allows you to link your scripts with the Project Explorer.

By toggling the button in the Project Explorer view, open scripts will show their corresponding folder in the Project Explorer when clicked on. Notice how the script highlighted in the Project Explorer changes as we click on different scripts in the script window.

This feature helps keep your different ‘DESCRIPTION’ and ‘server.R’ files sorted when developing multiple R Packages or Shiny applications.

Defining and Selecting Working Sets

As the number of projects grows larger, it may not be desirable to have all of your projects displayed at once. Working Sets are subsets of projects that you can define and switch between.

In our hypothetical example, we have four projects, and want to define two of them as school projects. If we assign them to a working set, we will see only those two projects while hiding the others.

Here we add the ’epidemiology’ and ‘regressionAnalysis’ projects to the ‘school’ working set. When we select this working set, only these projects are displayed in the Project Explorer.

To see all projects again, click the carrot in the Project Explorer view and choose Deselect Working Set.

Console

The Console is your window for processing all R commands. Previously we discussed different methods of evaluating code in the console. In this section, we’ll take a closer look at some of the console view functionalities.

Restarting, Cancelling, Terminating

There is a toolbar at the top of the console. The leftmost buttons are for used to interact with a current running console.

: restart console in the current working directory
: cancel the currently running task. Click this to manually end an in-progress command. Your console will display the text <processing> in the top right corner if a task is running, and <idle> otherwise. Note that you may need to increase the width of your console to see this text (see below).

: terminate the current R console. Effectively, this button just calls the R command ‘q()’.
: remove a terminated console. After you’ve terminated a console, it will remain open. Clicking this button removes the terminated console entirely.
: remove all terminated consoles.

Managing Multiple Consoles

Architect allows you to have multiple instances of the console running in parallel. To start an additional console, simply click the button on the top Architect toolbar. Once you have multiple consoles running, the console switcher will become illuminated. There are two buttons here:

: cycle through all open consoles, one at a time
: opens a drop-down menu with all open consoles. This is particularly useful when you have a large number of consoles open.

R Graphics View

Architect comes with an embedded R Graphics viewer. The first time you make a graph in the default device, the R Graphics viewer should open automatically. But if you’ve closed it for some reason, it can be reopened via Window > Show View > Other > StatET > R Graphics.

Sometimes when making a graph, you’ll find that the produced graph isn’t properly scaled to the R Graphics device. To rescale, click the button, and the plot will resize to the current window’s dimensions.

Alternatively, you can use a non-embedded graphics device which does not need to be frequently rescaled. For instructions on configuration, see the section Non-Embedded R Graphics View.

Object Browser

One of Architect’s unique features is a view called the Object Browser. Think of it as a visual representation of an ls() call.

The object browser allows you to inspect defined objects in your current R session. This view lets you preview the structure of complex objects, and track changes to the elements of your R session on the fly. Right clicking on an object brings up additional options, like printing the object to the R Console or taking a closer look with Architect’s data viewer. See the Object Browser in action below:

Documentation: Generating Reports

Mon, 01 Jan 0001 00:00:00 +0000

Architect ships with built-in functionality for creating and editing LaTeX, Sweave and Rmarkdown documents. In this section, we discuss how to use the basic functionality, but for instructions on how to configure your external tools, please refer to the Advanced section.

To create a Sweave, textile or Rmarkdown file, right click on a project and select New >. This will open a selection of available file types.

Rmarkdown Documents

Once you’ve created an Rmarkdown file, Architect will look something like this:

You’ll notice that syntax highlighting works automatically, and the Outline view gives a clear overview of our document’s structure.

In order to generate an html report based on a .Rmd file, open an R console in that file’s directory, then run the following code:

# install.packages("rmarkdown")
library(rmarkdown)
render("fileName.Rmd")

Sweave Documents

Like with Rmarkdown, Architect natively supports Sweave document development with syntax highlighting and Outline functionality.

Additionally, Architect offers specialized content assist when a Sweave document is open in the editor. As an example, type ‘<’, and Architect will give options for automatically creating a new code chunk.

In order to generate a .pdf file from a Sweave document, click on the .Rnw file in the Project Explorer and then select sweave-pdf from the External Tools () dropdown menu in the top toolbar. If your file is properly written, this will create various files (.tex, .log, etc.) as well as a .pdf render of your report.

Customizing Sweave Configuration

You can define your own Sweave configuration in the Sweave Document Processing (LaTeX + R) section of the External Tool Configuration window.

Click the New launch configuration button () in the top-left corner to define a new configuration.

Documentation: Tips and Tricks

Mon, 01 Jan 0001 00:00:00 +0000

Customizing Keyboard Shortcuts

All keyboard shortcuts can be rebound in Architect. To do so, select Window > Preferences > General > Keys, then select and rebind the desired command.

Content Assist

One of the most useful features in Architect is the intelligent content assist tool. Suppose we wanted to convert a string to a date. We would assume such a command had the words “as” and “date” in the name, but is it ‘as.date’, ‘asDate’, ‘as_date’…

Google no more. In Architect, whenever you’re stuck, type Ctrl + Space and a list of context-sensitive suggestions will pop up.

Above, we type in ‘asDate’, then Ctrl + Space, and content assist gives us the rest. It works for variable names and function parameter names too!

Quick Search

If you’re not sure where something is (or just want to get to it quickly), use the Quick Search tool. Type Ctrl + 3 and a search window will pop up. From there, type something like ‘font’ or ‘git’, and you’ll be presented with a list of relevant options.

Finding Function Definitions

As your workspace and projects become more complex, it can be difficult to find where various functions are defined. By selecting clicking on a function call with Ctrl + Left Click (or, alternatively, F3), Architect will jump directly to that function’s definition.

Renaming all instances of a variable

To quickly rename all instances of a variable, put your text cursor on the variable and type Ctrl + 1. Then type the new name, press Enter, and all other instances of that variable will be updated.

Note that these replacements are intelligently context sensitive. Instances of a variable inside of a function will not be affected when you rename a variable with the same name outside of the function.

Proper indentation of script

When programming, Architect will do its best to automatically properly indent your code, but sometimes things still get out of line. To make sure your entire script is properly indented, highlight all of the text with Ctrl + a, then type Ctrl + i.

R Package Manager

Architect ships with a dedicated tool for managing R packages. To access it, click on the white arrow () inside of the Console and select Open Package Manager.

Repositories Tab

The Repositories tab allows you to configure which repositories will have their packages listed in the Packages tab of the R Package Manager.

Note that the list of repositories can be edited or added to by clicking the preferences link in the screenshot above.

Packages Tab

The Packages tab gives you an overview of the R Packages in your environment, and allows you to install new ones or update existing packages. In the previous section, we added Bioconductor to our list of repositories, which allows us to now search for and install Bioconductor packages (e.g. Biobase) from this menu.

Clicking on a package will also provide information about a package’s dependencies and reverse dependencies.

Options Tab

Lastly, the Options tab allows you to select whether you’d like package from the ‘Suggests’ field to also be installed during installation.