HistoImagePlot
This is the development version of HistoImagePlot; to use it, please install the devel version of Bioconductor.
Plotting functionality for Histopathology pipeline datasets
Bioconductor version: Development (3.23)
Create side-by-side visualizations of tissue thumbnail image and HoverNet cell segmentation with colored cell type labels. Functionality automatically retrieves the thumbnail image associated with a HoverNet JSON file and overlays the segmentation data. This package is intended for researchers working with histopathological images, facilitating exploratory analysis, and integrates with the imageFeatureTCGA Bioconductor package.
Author: Ilaria Billato [aut, cre] (ORCID:
, affiliation: Department of Biology, University of Padova)
Maintainer: Ilaria Billato <ilaria.billato at phd.unipd.it>
citation("HistoImagePlot")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("HistoImagePlot")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("HistoImagePlot")| HistoImagePlot | HTML | R Script |
| Reference Manual |
Details
| biocViews | Software, Spatial, Visualization |
| Version | 0.99.10 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | BiocBaseUtils, cowplot, ggplot2, grDevices, imageFeatureTCGA, methods, RColorBrewer, S4Vectors, SpatialExperiment, SummarizedExperiment |
| System Requirements | |
| URL | https://github.com/waldronlab/HistoImagePlot |
| Bug Reports | https://github.com/waldronlab/HistoImagePlot/issues |
See More
| Suggests | anndataR, BiocStyle, dplyr, knitr, magick, rmarkdown, tinytest |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | HistoImagePlot_0.99.10.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | |
| macOS Binary (sonoma-arm64) | HistoImagePlot_0.99.10.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/HistoImagePlot |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/HistoImagePlot |
| Bioc Package Browser | https://code.bioconductor.org/browse/HistoImagePlot/ |
| Package Short Url | https://bioconductor.org/packages/HistoImagePlot/ |
| Package Downloads Report | Download Stats |