improve interactive plot

src/harpy/reports/Leviathan.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Leviathan Structural Variant Calling Summary"
+title: "Structural Variant Calling Summary (LEVIATHAN)"
 date: "`r format(Sys.time(), '%d %b, %Y at %H:%M')`"
 output:
   flexdashboard::flex_dashboard:

src/harpy/reports/LeviathanPop.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "Leviathan Structural Variant Calling Summary"
+title: "Structural Variant Calling Summary (LEVIATHAN)"
 date: "`r format(Sys.time(), '%d %b, %Y at %H:%M')`"
 output:
   flexdashboard::flex_dashboard:

src/harpy/reports/Naibr.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "NAIBR Structural Variant Calling Summary"
+title: "Structural Variant Calling Summary (NAIBR)"
 date: "`r format(Sys.time(), '%d %b, %Y at %H:%M')`"
 output:
   flexdashboard::flex_dashboard:
@@ -267,12 +267,11 @@ You may click on the plot to expand it in your browser window. Clicking it again
 out of the zoomed view.
 
 ```{r}
-justcolors <- c("#4a9fea", "#5a8c84", "#ffd75f")
-
-data.frame(x = 1, y = 1:3, colour = c("Inversion", "Deletion","Duplication")) %>% 
+color.palette <- c("deletion" = "#5a8c84", "duplication" = "#ffd75f", "inversion" = "#4a9fea")
+data.frame(x = 1, y = 1:3, colour = c("inversion", "deletion","duplication")) %>% 
 ggplot(aes(x, y, fill = colour))+
   geom_point(alpha=0, shape = 22, color = "white")+ # completely transparent rectangular point 
-  scale_fill_manual(values=justcolors, drop=FALSE) +
+  scale_fill_manual(values=color.palette, drop=FALSE) +
   guides(fill = guide_legend(override.aes = list(alpha=1, size = 25)))+ # showing the point in the legend
   theme(axis.title = element_blank(),
         axis.text = element_blank(),
@@ -388,36 +387,23 @@ allowing you to hover over a variant to provide additional information, includin
 number of haplotag barcodes supporting the variant.
 
 ```{r colors, echo = FALSE, warning = FALSE, message = FALSE}
-color.palette <- c(
-  "deletion" = "#5a8c84",
-  "duplication" = "#ffd75f",
-  "inversion" = "#4a9fea"
-)
-
 sv$ystart <- case_when(
   sv$SV == "inversion" ~ 0.1,
   sv$SV == "duplication" ~ 1.1,
   sv$SV == "deletion" ~ 2.1
 )
 sv$ystop <- sv$ystart + 0.8
+
+figheight <- nrow(fa.sizes) * 160
 ```
 
-```{r}
-l <- list()
-#nplotrows <- 0
-for (i in 1:nrow(fa.sizes)) {
-  sv.filt <- sv %>% filter(Chr1 == fa.sizes$contig[i])
-  sv_stats <- group_by(sv.filt, SV) %>% summarise(n = length(SV))
-  if (nrow(sv_stats) == 0) {
-    next
-  }
-  plt <- sv.filt %>%
-    ggplot() +
+```{r interactive_plot, fig.height=figheight}
+plt <- ggplot(sv) +
     geom_rect(
       alpha = 0.7,
       aes(
-        xmin = Break1,
-        xmax = Break2,
+        xmin = Break1/1000000,
+        xmax = Break2/1000000,
         ymin = ystart,
         ymax = ystop,
         fill = SV,
@@ -439,28 +425,14 @@ for (i in 1:nrow(fa.sizes)) {
       strip.text = element_text(color = "grey20"),
       legend.position = "none",
     ) +
+    coord_cartesian(xlim = c(0, NA), expand = F) +
     scale_x_continuous(labels = scales::comma) +
-    coord_cartesian(xlim = c(0, fa.sizes$size[i] + 1), expand = F) +
     scale_y_continuous(
       breaks = c(0.5, 1.5, 2.5),
       labels = c("INV", "DUP", "DEL"),
       limits = c(0,3)
     ) +
-    xlab("Position (bp)")
-    annotations <- list( 
-      x = 0.5,
-      y = 1.05,  
-      text = as.character(fa.sizes$contig[i]),  
-      xref = "paper",  
-      yref = "paper",  
-      xanchor = "center",  
-      yanchor = "bottom",  
-      showarrow = FALSE 
-    )
-    l[[i]] <- subplot(ggplotly(plt, height = 800, tooltip = "text"))
-}
+    xlab("Position (Mbp)")
 
-# remove null
-l <- Filter(Negate(is.null), l)
-subplot(l, nrows = length(l) , shareX = FALSE, titleX = TRUE)
+ggplotly(plt, height = figheight, tooltip  = "text", margin = list(l = 50, r = 50, b = 100, t = 100, pad = 1))
 ```

src/harpy/reports/NaibrPop.Rmd

@@ -1,5 +1,5 @@
 ---
-title: "NAIBR Structural Variant Calling Summary"
+title: "Structural Variant Calling Summary (NAIBR)"
 date: "`r format(Sys.time(), '%d %b, %Y at %H:%M')`"
 output:
   flexdashboard::flex_dashboard: