CellMorphR v3.1.2

Bug-fix release from a full code-path scan of the app.

Fixes

• Log transform on negative measurements. The log transform used log(x + 1) whenever any value was <= 0, which still produces NaN for values below -1. Orientation in real morphometry exports runs to about -5, so every log-transformed analysis silently dropped those cells. The data is now shifted so its minimum maps to 1 before the log.
• Effect Sizes with a single condition rendered an empty, warning-laden plot; it now explains that a second condition is needed.
• Removed a dead read of a control that no longer exists.

Verified by a static UI/server cross-reference of every input and output ID, plus a deep functional pass over every chart type, every export format (PDF, PNG, SVG, TIFF, EPS, PPTX), session save/load, demo data, column mapping and single-condition edge cases. All suites pass.

Download CellMorphR-v3.1.2.zip, unzip, and double-click run_cellmorphr.bat (Windows), Run CellMorphR.command (macOS) or ./run.sh (Linux) - or open CellMorphR.Rproj in RStudio and click Run App.

CellMorphR v3.1.1

Choose your own point shapes.

Download and run

Grab CellMorphR-v3.1.1.zip, unzip, then double-click run_cellmorphr.bat (Windows), Run CellMorphR.command (macOS) or ./run.sh (Linux) - or open CellMorphR.Rproj / app.R in RStudio and click Run App.

What's new

Point shapes were fixed in code, so neither the points nor the legend could be changed. Now, in Distributions > SuperPlot Options:

• pick the shape for each biological replicate - filled, solid or open circles, squares, triangles and diamonds, plus, cross, asterisk
• pick a separate shape for the individual cell points
• the legend follows your choice automatically

Applied consistently across violin, strip, sina, box+strip and dot plots, in both the dodged and sample-label layouts.

Everything from v3.1.0 is included: the in-app Guide tab with Quick Start, Check My Data, Script Builder and Statistics Help, plus the rewritten README covering all ten tabs.

CellMorphR v3.1.0

Interactive in-app guide, a data checker, and a script builder that writes your analysis for you.

Download and run

Grab CellMorphR-v3.1.0.zip, unzip, then either double-click run_cellmorphr.bat (Windows) / Run CellMorphR.command (macOS) / ./run.sh (Linux), or open CellMorphR.Rproj or app.R in RStudio and click Run App.

What's new

New Guide tab - interactive documentation inside the app

• Quick Start - the five steps from loading data to exporting a figure
• Check My Data - a plain-language report of what the app detected: how many samples and measurements, whether you have a time course, and a verdict on your replicate design. Three or more replicates per group is fine; two is flagged as weak with the reasons and better alternatives; one is flagged as untestable; unbalanced replicate counts are called out
• Script Builder - choose your measurement, grouping, statistical unit, test, correction, figure type and format, optionally loop over every measurement or add a dose-response trend test, then generate a complete R script and copy or download it
• Statistics Help - which test, which correction, how many replicates you need, and what to report

The generated script sources CellMorphR_v3.R, so it reuses the app's own validation, replicate summarising, pairwise tests and publication theme. The numbers and the figure match what you saw in the app exactly. Use it to re-run an analysis when data is updated, batch over many measurements, or attach a reproducible script to a paper.

analysis_template.R ships the same starting point as a plain file.

Documentation

The README's user guide was still describing the six tabs of v1.0. It now covers all ten tabs, plus figure editing (double-click to rename samples and timepoints), every export format including editable PowerPoint, the statistical guardrails, and scripting.

CellMorphR v3.0.1

Example datasets, optional timepoints, and renameable sample/timepoint labels.

Download and run

Grab CellMorphR-v3.0.1.zip, unzip, and double-click run_cellmorphr.bat (Windows), Run CellMorphR.command (macOS) or ./run.sh (Linux). The bundle now includes two example datasets you can load straight from the Data tab.

What's new

Know how to format your data

• Two example datasets ship with the app: example_data.csv (time course - 4 conditions x 4 timepoints x 3 biological replicates) and example_data_no_timepoints.csv (single snapshot - 4 samples x 3 replicates)
• New DATA_FORMAT.md: required vs optional columns, worked examples for both designs, and the design choices that affect your statistics

Timepoints are now optional

• Previously Time_min was required, so single-snapshot experiments could not be loaded at all. Leave the column out and the app compares your samples directly, with the samples on the x axis and nothing labelled "min"
• The column-mapping dialog offers "(no timepoints - compare samples directly)"
• Distributions, ridge plots, ECDF/histogram faceting and the significance brackets all adapt to a design with no time axis
• The Trajectories tab explains itself instead of drawing a meaningless single-point plot

Rename what appears on the graph

• Timepoint labels are now editable - call them "0 h", "Uninduced", "Pre-treatment" - from the Data sidebar or by double-clicking any figure
• The underlying time stays numeric, so ordering, trajectories and the dose-response trend test are unaffected
• Condition/sample renaming (already in v3.0.0) sits alongside it; both apply across every figure, table and export

Fix

• Significance brackets parsed the numeric time back out of the axis label text, which broke as soon as a timepoint was renamed or the data had no time column at all

CellMorphR v3.0.0

Publication-ready figures, editable output, and hardened statistics.

Download and run

Grab CellMorphR-v3.0.0.zip, unzip it, and double-click:

OS	Double-click
Windows	run_cellmorphr.bat
macOS	Run CellMorphR.command
Linux	./run.sh

The first run installs the required R packages (a few minutes); after that the app opens in your browser instantly. R must be installed: https://cran.r-project.org

What's new

Figures

• SuperPlot options: shape-coded replicate dots, cells colored by biological replicate, per-group n on the axis - show sample-to-sample variation without needing p-values
• Double-click any figure to edit its title, axis labels, legend title, caption, and condition names in place; renames apply across every tab, table, and export
• Editable vector export: PDF, SVG, EPS, TIFF, PNG, plus PowerPoint (officer/rvg) where text and shapes stay editable, and a per-panel PPTX deck from the Pub Figure tab
• Custom labels, fonts, sizes, colors, and point geometry on every plot tab

Statistics

• Significance brackets now follow the test and correction chosen on the Statistics tab, so figures and tables always agree
• 95% confidence intervals and degrees of freedom in the pairwise table
• Small-n guardrails: the app warns when Wilcoxon cannot reach p<0.05 for the available replicate counts (n=2 vs 2 has a minimum attainable p of 0.33)
• New dose-response trend test: fits replicate summaries against a numeric predictor per stratum with slope, 95% CI, p and R-squared
• Split Condition labels such as pSJExD_gp75_100nM into vector and numeric dose columns for factorial and gradient designs
• All hypothesis tests continue to run on biological-replicate summaries, never on individual cells

Layout and fixes

• All 48 figure variants audited and fixed for overlapping text: wrapped titles, subtitles, captions and legend entries; stacked legends; brackets capped per timepoint; adaptive axis-label wrapping
• Repaired plots that previously failed to build: Effect Sizes, the EMM plot, and the Cell Metrics heatmap
• Fixes to log scales, bracket vs manual Y limits, EPS export without cairo, session restore, and PCA loading labels

See METHODS.md for a citable description of the plotting and statistics.

CellMorphR v1.0.0 (archived)

The original single-file CellMorphR app (6 analysis tabs), kept for reference and reproducibility.

Archived and unmaintained - it does not receive fixes. Use v3.0.0 for current work.

Run it with:

shiny::runApp(shiny::shinyAppFile("CellMorphR_v1.0.R"), launch.browser = TRUE)

Also available in the repository at archive/CellMorphR_v1.0.R.