update panel labels on figure 4

Author: Aariq

R/6-simulation-figures.Rmd

@@ -272,7 +272,9 @@ Put three scenarios together to make a figure.
 
 ```{r fig.width=9.5, fig.height=2.833}
 r1 <-
-  (none.cor.p | apparent.cor.p | hidden.cor.p) +
+  (none.cor.p +       annotate("text", x = -Inf, y = Inf, label = "(a)", hjust = -0.2, vjust = 1.2) |
+     apparent.cor.p + annotate("text", x = -Inf, y = Inf, label = "(b)", hjust = -0.2, vjust = 1.2)|
+     hidden.cor.p +   annotate("text", x = -Inf, y = Inf, label = "(c)", hjust = -0.2, vjust = 1.2)) +
   plot_layout(guides = "collect") &
   #center subtitles
   theme(plot.subtitle = element_text(hjust = 0.5))
@@ -282,7 +284,9 @@ r1
 
 ```{r fig.width=9.5, fig.height=2.833}
 r2 <-
-  (none.pca.p | apparent.pca.p | hidden.pca.p) &
+  (none.pca.p +       annotate("text", x = -Inf, y = Inf, label = "(d)", hjust = -0.2, vjust = 1.2)| 
+     apparent.pca.p + annotate("text", x = -Inf, y = Inf, label = "(e)", hjust = -0.2, vjust = 1.2) | 
+     hidden.pca.p +   annotate("text", x = -Inf, y = Inf, label = "(f)", hjust = -0.2, vjust = 1.2)) &
   scale_y_continuous(expand = expansion(mult = c(0.12, 0.05))) &
   theme(legend.position = "none")
 r2
@@ -291,19 +295,17 @@ r2
 
 ```{r fig.width=9.5, fig.height=2.833}
 r3 <-
-  (none.pls.p | apparent.pls.p | hidden.pls.p) &
+  (none.pls.p +       annotate("text", x = -Inf, y = Inf, label = "(g)", hjust = -0.2, vjust = 1.2)| 
+     apparent.pls.p + annotate("text", x = -Inf, y = Inf, label = "(h)", hjust = -0.2, vjust = 1.2)|
+     hidden.pls.p +   annotate("text", x = -Inf, y = Inf, label = "(i)", hjust = -0.2, vjust = 1.2)) &
   scale_y_continuous(expand = expansion(mult = c(0.12, 0.05))) &
   theme(legend.position = "none")
 r3
 ```
-Can't get tags inside of plots with patchwork
+Can't get tags inside of plots with patchwork, using `annotate()` instead
 
 ```{r fig.width=9.5, fig.height=8.5}
-(r1/r2/r3)  & plot_annotation(tag_levels = "a", tag_suffix = ")") &
-  theme(
-    plot.tag.position = c(0,1),
-    plot.tag = element_text(vjust = 3, hjust = 0)
-  )
+(r1/r2/r3) 
 ```
 
 

out/simulation biplots.png

@@ -9,7 +9,7 @@
     ]
   },
   "Bioconductor": {
-    "Version": "3.11"
+    "Version": "3.12"
   },
   "Packages": {
     "BH": {
@@ -84,10 +84,10 @@
     },
     "Matrix": {
       "Package": "Matrix",
-      "Version": "1.2-18",
+      "Version": "1.3-0",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "08588806cba69f04797dab50627428ed"
+      "Hash": "a308a28fe951c437957ffe20c84e6b66"
     },
     "MatrixModels": {
       "Package": "MatrixModels",
@@ -283,10 +283,10 @@
     },
     "codetools": {
       "Package": "codetools",
-      "Version": "0.2-16",
+      "Version": "0.2-18",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "89cf4b8207269ccf82fbeb6473fd662b"
+      "Hash": "019388fc48e48b3da0d3a76ff94608a8"
     },
     "colorspace": {
       "Package": "colorspace",
@@ -388,10 +388,10 @@
     },
     "foreign": {
       "Package": "foreign",
-      "Version": "0.8-80",
+      "Version": "0.8-81",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "ae1b1e15cc6ccb2bc61c0ac33e86d35f"
+      "Hash": "74628ea7a3be5ee8a7b5bb0a8e84882e"
     },
     "fs": {
       "Package": "fs",
@@ -695,10 +695,10 @@
     },
     "nlme": {
       "Package": "nlme",
-      "Version": "3.1-149",
+      "Version": "3.1-151",
       "Source": "Repository",
       "Repository": "CRAN",
-      "Hash": "7c24ab3a1e3afe50388eb2d893aab255"
+      "Hash": "42c8ba2b6a32a6bf0874e93e3bd86a43"
     },
     "nloptr": {
       "Package": "nloptr",