v1.3.0

Changelogs:

• Added utils.R to keep internal reusable functions.
• Refactored run.flowsom:
  • Added verbose parameter to optionally print progress messages.
  • Overwrites clust.name and meta.clust.name columns in input data.table
    if they already exist.
  • Tidied up and simplified code.
• Updated run.umap to overwrite umap.x.name and umap.y.name columns in
  input data.table if they already exist.
• Updated do.asinh:
  • Overwrite columns in input data.table if they already exist.
  • Added support to specify a list of cofactors, so different values can be assigned to different markers.
• Refactored make.colour.plot:
  • Move some code out to internal functions for modularity.
  • Rewrote and simplified code.
  • Added more colour scheme options to support all options in viridis and RColorBrewer and jet.
  • Updated documentation.
  • Fixed issue #197 by using geom_label_repel to draw centroid labels.
  • Added option to do fast plot using scattermore.
• Added deprecated message for fast.colour.plot.
• Fixed package.check for issue #186.
• Refactored read.files and remove any setwd() for issue #162.
• Add add.label to multi.plot for issue #202.
• Added a NEWS.md file to track changes to the package.
• Added testthat unittests.

v1.2.0

Major updates to Spectre in v1.2.0.

Highlights:

• Greatly simplified package dependencies
• Reduction in the size of internally stored datasets. Data moved to https://github.com/ImmuneDynamics/data
• Fast UMAP implementation (run.umap)
• Fast plotting options (fast.colour.plot and fast.multi.plot)
• Fast generation of summary statistics (create.sumtable)
• Batch integration methods with rPCA (run.rpca)
• Minor fixes in CytoNorm and spatial workflows
• Inclusion of CI tests

R session information at time of release:

Mac:

• OS: macOS Ventura 13.5.2
• R version: v4.4.0 (2024-04-24)
• RStudio version: 2024.04.1+748

To install:, please see our instructions on our getting started page.

What's Changed

• Update Spectre rPCA.R by @tomashhurst in #191
• Add CI by @ghar1821 in #192
• Updating v1.1.0 to v1.2.0 by @tomashhurst in #194

Full Changelog: v1.1.0...v1.2.0

v1.1.0

In v1.1 we have removed the package dependencies rgeos and rgdal as these are no longer available on CRAN. The package should install fine without these dependencies, but some spatial functions may not work properly. If required, one can download the archived packages, unzip them, and then placed them in the R library location.

To install, please see our instructions on our getting started page.

R session information at time of release:

Mac:

• OS: macOS Catalina 10.15.7
• R version: v4.3.4 (2023-10-31)
• RStudio version: 2023.3.0.386

v1.0.0

---

Installation: to install this version using R or Docker, see our getting started page.

Updates:

• Major updates to our spatial analysis functions and workflows
• Re-organisation of workflow folders structures

R session information at time of release:

Mac:

• OS: macOS Catalina 10.15.7
• R version: v4.1.1 (2021-08-10)
• RStudio version: v1.4.1717

Windows:

• OS: Windows 10 x64
• R version: v4.1.0 (2021-05-24)
• RStudio version: v1.4.1717

v0.5.5

---

Installation: to install this version using R or Docker, see our getting started page.

Updates:

• Fixes to issues created by the update to CytoNorm

R session information at time of release:

Mac:

• OS: macOS Catalina 10.15.7
• R version: v4.1.0 (2021-05-24)
• RStudio version: v1.4.1717

Windows:

• OS: Windows 10 x64
• R version: v4.1.0 (2021-05-24)
• RStudio version: v1.4.1717

v0.5.4

---

Installation: to install this version, see our getting started page.

Updates:

• Updates to the installation process -- specifically removing hdf5r dependency, which is not required and necessitated additional brewer installations, and replaced it with rhdf5 from Bioconductor.

R session information at time of release:

Mac:

• OS: macOS Catalina 10.15.7
• R version: v4.1.0 (2021-05-18)
• RStudio version: v1.4.1717

Windows:

• OS: Windows 10 x64
• R version: v4.1.0 (2021-05-18)
• RStudio version: v1.4.1717

v0.5.3

---

Installation: to install this version, see our getting started page.

Updates:

• Updates to the do.create.outlines function for dealing with polygon shapes and cell masks.
• Updates to the package.check function for clarity.

R session information at time of release:

Mac:

• OS: macOS Catalina 10.15.7
• R version: v4.1.0 (2021-05-18)
• RStudio version: v1.4.1717

Windows:

• OS: Windows 10 x64
• R version: v4.1.0 (2021-05-18)
• RStudio version: v1.4.1717

v0.5.2

---

Installation: to install this version, see our getting started page.

Updates:

• Updates and improvements relating to the installation of dependencies.
• Fixes for spatial analysis functions.
• Modifications to make.colour.plot defaults to improve visualisation for figures.

R session information at time of release:

Mac:

• OS: macOS Catalina 10.15.7
• R version: v4.1.0 (2021-05-18)
• RStudio version: v1.4.1717

Windows:

• OS: Windows 10 x64
• R version: v4.1.0 (2021-05-18)
• RStudio version: v1.4.1717

v0.5.1

Fixes for spatial analysis functions.

v0.5.0

Major update -- spatial analysis functions incorporated directly in Spectre.