Merge pull request satijalab#2620 from mfansler/patch-mf

Consistent `FeaturePlot` axis limits
zgyaru · Feb 20, 2020 · 31378a5 · 31378a5
2 parents 8b55a01 + c208359
commit 31378a5
Show file tree

Hide file tree

Showing 2 changed files with 39 additions and 12 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.1.3.9004
-Date: 2020-02-13
+Version: 3.1.3.9005
+Date: 2020-02-20
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details.
 Authors@R: c(

diff --git a/R/visualization.R b/R/visualization.R
@@ -1164,7 +1164,10 @@ FeaturePlot <- function(
         if (j == length(x = features) && !blend) {
           suppressMessages(
             expr = plot <- plot +
-              scale_y_continuous(sec.axis = dup_axis(name = ident)) +
+              scale_y_continuous(
+                sec.axis = dup_axis(name = ident),
+                limits = ylims
+              ) +
               no.right
           )
         }
@@ -1238,6 +1241,7 @@ FeaturePlot <- function(
                 yes = levels(x = data$split)[ii],
                 no = ''
               )),
+              limits = ylims,
               expand = c(0, 0)
             ) +
             labs(
@@ -1290,34 +1294,57 @@ FeaturePlot <- function(
             expr = x +
               theme_cowplot() +
               ggtitle("") +
-              scale_y_continuous(sec.axis = dup_axis(name = "")) +
+              scale_y_continuous(sec.axis = dup_axis(name = ""), limits = ylims) +
               no.right
           ))
         }
       )
       nsplits <- length(x = levels(x = data$split))
       idx <- 1
       for (i in (length(x = features) * (nsplits - 1) + 1):(length(x = features) * nsplits)) {
-        plots[[i]] <- suppressMessages(plots[[i]] + scale_y_continuous(sec.axis = dup_axis(name = features[[idx]])) + no.right)
+        plots[[i]] <- suppressMessages(
+          expr = plots[[i]] +
+            scale_y_continuous(
+              sec.axis = dup_axis(name = features[[idx]]),
+              limits = ylims
+            ) +
+            no.right
+        )
         idx <- idx + 1
       }
       idx <- 1
       for (i in which(x = 1:length(x = plots) %% length(x = features) == 1)) {
-        plots[[i]] <- plots[[i]] + ggtitle(levels(x = data$split)[[idx]]) + theme(plot.title = element_text(hjust = 0.5))
+        plots[[i]] <- plots[[i]] +
+          ggtitle(levels(x = data$split)[[idx]]) +
+          theme(plot.title = element_text(hjust = 0.5))
         idx <- idx + 1
       }
       idx <- 1
       if (length(x = features) == 1) {
         for (i in 1:length(x = plots)) {
-          plots[[i]] <- plots[[i]] + ggtitle(levels(x = data$split)[[idx]]) + theme(plot.title = element_text(hjust = 0.5))
+          plots[[i]] <- plots[[i]] +
+            ggtitle(levels(x = data$split)[[idx]]) +
+            theme(plot.title = element_text(hjust = 0.5))
           idx <- idx + 1
         }
+        idx <- 1
+        if (length(x = features) == 1) {
+          for (i in 1:length(x = plots)) {
+            plots[[i]] <- plots[[i]] + ggtitle(levels(x = data$split)[[idx]]) + theme(plot.title = element_text(hjust = 0.5))
+            idx <- idx + 1
+          }
+        }
+        plots <- plots[c(do.call(
+          what = rbind,
+          args = split(x = 1:length(x = plots), f = ceiling(x = seq_along(along.with = 1:length(x = plots))/length(x = features)))
+        ))]
+        plots <- wrap_plots(plots, ncol = nsplits)
+      } else {
+        plots <- wrap_plots(plots, ncol = ncol, nrow = split.by %iff% length(x = levels(x = data$split)))
+      }
+      if (!is.null(x = legend) && legend == 'none') {
+        plots <- plots & NoLegend()
       }
-      plots <- plots[c(do.call(
-        what = rbind,
-        args = split(x = 1:length(x = plots), f = ceiling(x = seq_along(along.with = 1:length(x = plots))/length(x = features)))
-      ))]
-      plots <- wrap_plots(plots, ncol = nsplits)
     } else {
       plots <- wrap_plots(plots, ncol = ncol, nrow = split.by %iff% length(x = levels(x = data$split)))
     }