diff --git a/DESCRIPTION b/DESCRIPTION index 4b56234a..2685b35c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: celda Title: CEllular Latent Dirichlet Allocation -Version: 1.7.1 +Version: 1.7.3 Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu", role = c("aut", "cre")), person("Sean", "Corbett", email = "scorbett@bu.edu", role = c("aut")), @@ -8,8 +8,14 @@ Authors@R: c(person("Joshua", "Campbell", email = "camp@bu.edu", person("Shiyi", "Yang", email="syyang@bu.edu", role = c("aut")), person("Eric", "Reed", email="reeder@bu.edu", role = c("aut")), person("Zhe", "Wang", email="zhe@bu.edu", role = c("aut"))) -Description: Utilizing Bayesian hierarchical models to analyze single-cell genomic data. -Depends: R (>= 3.6) +Description: Celda is a suite of Bayesian hierarchical models for + clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to + perform "bi-clustering" and simultaneously cluster genes into gene modules + and cells into cell subpopulations. It also contains DecontX, a novel + Bayesian method to computationally estimate and remove RNA contamination in + individual cells without empty droplet information. A variety of scRNA-seq + data visualization functions is also included. +Depends: R (>= 4.0) VignetteBuilder: knitr Imports: plyr, foreach, ggplot2, RColorBrewer, grid, scales, gtable, grDevices, graphics, matrixStats, doParallel, digest, methods, diff --git a/R/perplexity.R b/R/perplexity.R index 7388701d..e011bc5b 100644 --- a/R/perplexity.R +++ b/R/perplexity.R @@ -851,7 +851,7 @@ setMethod("plotGridSearchPerplexityDiff", plot <- ggplot2::ggplot(dt[!is.na(perpdiffK), ], ggplot2::aes_string(x = "K", y = "perpdiffK")) + - ggplot2::geom_jitter(height = 0, width = 0.1, + ggplot2::geom_jitter(height = 0, width = 0.1, alpha = 0.5, ggplot2::aes_string(color = "L")) + ggplot2::scale_color_discrete(name = "L") + ggplot2::geom_path(data = diffMeansByK[!is.na(meanperpdiffK), ], @@ -859,7 +859,8 @@ setMethod("plotGridSearchPerplexityDiff", color = "L"), size = 1) + ggplot2::ylab("Perplexity difference compared to previous K") + ggplot2::xlab("K") + - ggplot2::scale_x_discrete(breaks = seq(as.integer(levels(dt$K))[2], + ggplot2::scale_x_discrete( + breaks = seq(min(as.integer(levels(dt$K))), max(as.integer(levels(dt$K))), sep)) + ggplot2::theme_bw() } else if (nlevels(dt$L) > 1) { @@ -885,7 +886,7 @@ setMethod("plotGridSearchPerplexityDiff", plot <- ggplot2::ggplot(dt[!is.na(perpdiffL), ], ggplot2::aes_string(x = "L", y = "perpdiffL")) + - ggplot2::geom_jitter(height = 0, width = 0.1, + ggplot2::geom_jitter(height = 0, width = 0.1, alpha = 0.5, ggplot2::aes_string(color = "K")) + ggplot2::scale_color_discrete(name = "K") + ggplot2::geom_path( @@ -895,7 +896,8 @@ setMethod("plotGridSearchPerplexityDiff", size = 1) + ggplot2::ylab("Perplexity difference compared to previous L") + ggplot2::xlab("L") + - ggplot2::scale_x_discrete(breaks = seq(as.integer(levels(dt$L))[2], + ggplot2::scale_x_discrete( + breaks = seq(min(as.integer(levels(dt$L))), max(as.integer(levels(dt$L))), sep)) + ggplot2::theme_bw() } else { @@ -945,13 +947,14 @@ setMethod("plotGridSearchPerplexityDiff", plot <- ggplot2::ggplot(dt[!is.na(perpdiffK), ], ggplot2::aes_string(x = "K", y = "perpdiffK")) + - ggplot2::geom_jitter(height = 0, width = 0.1) + + ggplot2::geom_jitter(height = 0, width = 0.1, color = "grey") + ggplot2::geom_path(data = diffMeansByK[!is.na(meanperpdiffK), ], ggplot2::aes_string(x = "K", y = "rollmean", group = 1), size = 1) + ggplot2::ylab("Perplexity difference compared to previous K") + ggplot2::xlab("K") + - ggplot2::scale_x_discrete(breaks = seq(as.integer(levels(dt$K))[2], + ggplot2::scale_x_discrete( + breaks = seq(min(as.integer(levels(dt$K))), max(as.integer(levels(dt$K))), sep)) + ggplot2::theme_bw() } else { @@ -1000,13 +1003,14 @@ setMethod("plotGridSearchPerplexityDiff", plot <- ggplot2::ggplot(dt[!is.na(perpdiffL), ], ggplot2::aes_string(x = "L", y = "perpdiffL")) + - ggplot2::geom_jitter(height = 0, width = 0.1) + + ggplot2::geom_jitter(height = 0, width = 0.1, color = "grey") + ggplot2::geom_path(data = diffMeansByL[!is.na(meanperpdiffL), ], ggplot2::aes_string(x = "L", y = "rollmean", group = 1), size = 1) + ggplot2::ylab("Perplexity difference compared to previous L") + ggplot2::xlab("L") + - ggplot2::scale_x_discrete(breaks = seq(as.integer(levels(dt$L))[2], + ggplot2::scale_x_discrete( + breaks = seq(min(as.integer(levels(dt$L))), max(as.integer(levels(dt$L))), sep)) + ggplot2::theme_bw() } else {