1.5.1版本变化小的改进和修复,更新readVisium正常工作时功能名称包括空白——解决w_i舍入和密度-添加细节装饰图案与spatialEnhance变化版本1.5.0新Bioconductor猛击(3.15)-版本编号变化与Bioconductor凹凸变化版本1.4.0新Bioconductor版本(3.14)-编号改变Bioconductor版本凹凸变化1.3.1小改进和修复,更新文档getRDS (), mcmcChain(),和spatialEnhance ()。1.3.0版本版本变化小的改进和修正,添加信息文档。- getRDS()更新与新URL。改变版本1.2.0新Bioconductor版本(3.12)-编号改变Bioconductor版本凹凸变化版本1.1.2小改进和修复——clusterPlot()接受字符作为标签的参数向量和因素。1.1.1版本变化小的改进和修复——spatialPreprocess()使用准确而不是默认近似PCA。变化版本1.1.0新Bioconductor猛击(3.13)——版本编号变更Bioconductor版本凹凸变化0.99.8小改进和修复——spatialCluster()和spatialEnhance()现在使用更快的实现多元正态密度,减少运行时的大约40%。版本0.99.7变化小的改进和修复,现在文档示例使用更少的迭代以减少R CMD的运行时检查。- qTune (), min_rep和max_rep参数与燃烧所取代。分别在nrep spatialCluster是一致的()。0.99.6版本新特性的变化- getRDS()获得一个缓存参数。当真实,RDS是使用BiocFileCache本地缓存。 Minor improvements and fixes - Addressed reviewer concerns (https://github.com/Bioconductor/Contributions/issues/1624) - Updated stop/warning/message statements to remove redundancies and unnecessary use of paste(). - Removed inline conditional statements. - Cache downloaded RDS in getRDS() (see above). - spatialCluster() and spatialEnhance() handle the edge case where only one iteration is kept after excluding burn-in. - The coda::mcmc object returned by mcmcChain() now specifies the thinning interval used in enhanced objects. - spatialCluster() and spatialEnhance() now include platform-specific defaults for the gamma parameter. - Minor internal refactoring. Changes in version 0.99.5 Minor improvements and fixes - In spatialCluster() and spatialEnhance(), setting burn.in equal to nrep now raises an error. Changes in version 0.99.4 New features - enhanceFeatures() now takes an nrounds parameter that corresponds to the same parameter in xgboost. If nrounds is set to 0, we automatically tune the parameter using a train/test split for improved feature prediction. - spatialCluster() and spatialEnhance() both gain a burn.in parameter specifying the number of MCMC iterations to exclude when aggregating cluster labels and enhanced PCs. - In clusterPlot(), label now accepts factors and vectors of strings, in addition to numeric vectors or a column name in colData. - Additional vignettes provided for reproducing the analyses of the melanoma, dorsolateral prefrontal cortex, and squamous cell carcinoma datasets presented in the bioRxiv manuscript. Minor improvements and fixes - The internal layout of subspots is now correctly oriented (accounting for vertical flip of spot coordinates) when using spatial plot functions on enhanced Visium data. - In spatialEnhance(), PCs are now averaged over the MCMC iterations (excluding the burn-in period). - In enhanceFeatures(), negative expression is now clipped to 0. - spatialPreprocess() now adds a boolean is.HVG column to rowData. - In featurePlot(), additional arguments to geom_polygon() are correctly passed through. Changes in version 0.99.3 Minor improvements and fixes - Updated README.md to include system requirements, additional installation details, and link to vignette with demonstration of package functions, per journal guidelines. Changes in version 0.99.2 Minor improvements and fixes - spatialEnhance() incorrectly added row offset to spot column coordinate when generating subspot colData, and vice versa. This resulted in subspots being reflected over y=x in spatial plots, and has been fixed. - Figures in the demonstration vignette have been updated with this fix. Changes in version 0.99.1 Minor improvements and fixes - Removed Maintainer field from DESCRIPTION to adhere to Bioconductor guidelines. Changes in version 0.99.0 New features - Initial Bioconductor submission