Merge pull request #321 from zhewa/master

Updates to plotGridSearchPerplexityDiff and description

DESCRIPTION

@@ -1,15 +1,21 @@
 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")),
     person("Yusuke", "Koga", email="ykoga07@bu.edu", role = c("aut")),
     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,

R/perplexity.R

@@ -851,15 +851,16 @@ 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), ],
                 ggplot2::aes_string(x = "K", y = "rollmean", group = "L",
                     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 {