Getting started

This chapter takes you from nothing to an exported figure: install, paste a small data set, describe it, test it, draw it, export it, save it. It takes about ten minutes.

Install

Every release is published on the releases page. Pick the file for your system. The names below are those of version 0.4.0; later versions change only the number.

Linux

The AppImage needs nothing installed:

curl -LO https://github.com/ZahakJ/dioptra/releases/latest/download/Dioptra_0.4.0_amd64.AppImage
chmod +x Dioptra_0.4.0_amd64.AppImage
./Dioptra_0.4.0_amd64.AppImage

If it refuses to start with a message about FUSE, your distribution does not ship libfuse2 by default (Ubuntu 22.04 and later). Install it (sudo apt install libfuse2), or use the .deb.

On Debian and Ubuntu:

curl -LO https://github.com/ZahakJ/dioptra/releases/latest/download/Dioptra_0.4.0_amd64.deb
sudo apt install ./Dioptra_0.4.0_amd64.deb

On Fedora and other rpm systems:

curl -LO https://github.com/ZahakJ/dioptra/releases/latest/download/Dioptra-0.4.0-1.x86_64.rpm
sudo dnf install ./Dioptra-0.4.0-1.x86_64.rpm

Windows

Download Dioptra_0.4.0_x64_en-US.msi and run it. Windows may show a SmartScreen notice because the installer is not signed with a paid certificate; choose More info, then Run anyway. Dioptra uses the WebView2 runtime that ships with Windows 10 and 11.

macOS

Download the .dmg for your processor (the Apple menu, About This Mac, says “Apple M…” for Apple silicon or “Intel” otherwise), open it and drag Dioptra into Applications. The app is ad-hoc signed but not notarized (there is no paid Apple certificate), so the first launch says “Apple could not verify Dioptra”. Control-click the app, choose Open, then Open again; on macOS 15 and later, open it once, then go to System Settings → Privacy & Security and click Open Anyway. Or run once in Terminal:

xattr -cr /Applications/Dioptra.app

macOS remembers the choice.

Paste your first data

Start Dioptra. You see an empty project: the project rail on the left (tables, analyses, graphs, layouts), the work area in the middle and the inspector on the right. The work area offers three ways in: paste data, open the bundled sample project (a cytokine study with a dose comparison, a dose-response fit and a survival curve, each with its analysis and figure), or open this manual.

Copy these three columns (from this page, a spreadsheet or a text file; tabs, commas and semicolons all work):

Control	Low dose	High dose
12.1	15.3	21.0
10.4	16.8	19.2
11.7	14.1	24.6
13.2	17.5	22.3
9.8	15.9	20.8
12.5	16.2	23.1

Choose File → Paste as new table (Ctrl-Shift-V; ⌘-Shift-V on a Mac). The dialog shows a preview, what it detected (separator, decimal mark, whether the first row is a header) and a suggested table kind with a small sketch of each kind. For three groups of replicate values the right kind is Column: each column is a group. Pick it, give the table a title such as “Plasma IL-6”, and press Create table.

Click any cell. The inspector says where it came from (“Pasted from the clipboard at …”). The status line at the bottom shows n, mean, SD and sum of the selection.

Describe it

Press Analyze (Ctrl-Shift-A). The list shows every analysis; those that do not fit a Column table are greyed with the reason. Choose Descriptive statistics and run it. The results sheet opens beside the table: one sentence per group in APA style, then the table of N, mean, SD, SEM, confidence interval, median and quartiles, then a short list headed Before you report this.

Test it

Press Analyze again and choose One-way ANOVA. The options panel holds the few choices that matter, each with one line on what it means: which groups, whether to use Welch’s ANOVA (which does not assume equal SDs), and which multiple comparisons to run (Tukey–Kramer for all pairs by default). Run it.

The sheet starts with the assumption checks: normality of residuals and equality of variances, each with its test result and what it means for this analysis. If one is in doubt it is open and amber, and it names the alternative (Welch’s ANOVA, or Kruskal–Wallis). Then the summary sentence, with the effect size and its confidence interval before the p value. Then the ANOVA table and the comparisons.

Change a number in the table. The sheet marks itself stale and recomputes when you look at it.

Draw it

On the results sheet press Make graph. Dioptra draws a column graph of the three groups with every data point shown, error bars, and a bracket for each comparison from the ANOVA, labelled in the project’s p-value style.

The graph is a live object. Click the Y axis title and the inspector shows its properties; type “IL-6 (pg/mL)”. Change the family to Box or Violin in the toolbar; the data and brackets follow. Choose a theme (Instrument, Night for slides, Journal for black-and-white print) and a palette.

Export it

Press Export (Ctrl-Alt-E). Choose PDF, SVG or PNG; set the size in millimetres or inches (85 × 70 mm is a single journal column); for PNG choose the resolution. The dialog states exactly what will be written, for example “1004 × 827 pixels at 300 dpi, 85 × 70 mm”. PDF embeds the fonts; SVG keeps text as text.

Save it

File → Save (Ctrl-S) writes a .dioptra file: the table, the formulas, both analyses, the graph and the history of what you did. Close Dioptra and open the file again; every result is recomputed from the data and comes out the same.

That is the whole loop. The rest of the manual explains each step in depth.