fixes

pdimens · Jul 10, 2024 · c712a66 · c712a66
1 parent 77e5c3b
commit c712a66
Showing 1 changed file with 37 additions and 34 deletions.
diff --git a/src/harpy/reports/HapCut2.Rmd b/src/harpy/reports/HapCut2.Rmd
@@ -163,22 +163,6 @@ to collapse the right tails for better readability.
 The table below provides details on the outcome of haplotype phasing on a per-contig basis.
 
 ## Per contig data
-### per contig plot {.no-title}
-```{r warning=FALSE, message=FALSE, echo= FALSE, fig.height=ridgeheight, fig.width=8}
-ggplot(df, aes(x = block_length, y = contig, fill = after_stat(x))) +
-  geom_density_ridges_gradient(scale = 1.4) +
-  scale_fill_viridis_c(option = "C", trans = "log10") +
-  theme_minimal() +
-  theme(legend.position = "none") +
-  scale_x_log10(
-     breaks = trans_breaks("log10", function(x) 10^x),
-     labels = trans_format("log10", math_format(10^.x))
-  ) +
-  labs(title = "Distribution of Haplotype Lengths by Contig", fill = "Haplotype Length (bp)") +
-  xlab("Haplotype Length (log scale)") +
-  ylab("")
-```
-
 ### stats per contig {.no-title}
 ```{r echo= FALSE, message = FALSE, warning = FALSE, out.width="100%"}
 percontig <- df %>% group_by(contig) %>% summarise(
@@ -200,6 +184,24 @@ DT::datatable(
   )
 ```
 
+## contig ridgeplot
+### per contig plot {.no-title}
+```{r warning=FALSE, message=FALSE, echo= FALSE, fig.height=ridgeheight, fig.width=8}
+ggplot(df, aes(x = block_length, y = contig, fill = stat(x))) +
+  geom_density_ridges_gradient() +
+  scale_fill_viridis_c(option = "C", trans = "log10") +
+  theme_minimal() +
+  theme(legend.position = "none") +
+  scale_x_log10(
+     breaks = trans_breaks("log10", function(x) 10^x),
+     labels = trans_format("log10", math_format(10^.x))
+  ) +
+  labs(title = "Distribution of Haplotype Lengths by Contig", fill = "Haplotype Length (bp)") +
+  xlab("Haplotype Length (log scale)") +
+  ylab("")
+```
+
+
 # Per-Sample Stats
 ## per sample desc
 ### stats per sample desc {.no-title}
@@ -213,23 +215,7 @@ Phasing typically results in extreme right-tails in these distributions, making
 visualization difficult to plot meaningfully. The plot presented below has 
 **log-scaled lengths** to collapse the right tails for better readability. 
 
-## per sample 
-### the ridgeplot {.no-title}
-```{r warning=FALSE, message=FALSE, echo= FALSE, fig.height=ridgeheight.samples, fig.width=8}
-ggplot(df, aes(x = block_length, y = sample)) +
-  geom_density_ridges_gradient(aes(fill = ..x..), scale = 1.4) +
-  scale_fill_viridis_c(option = "G", trans = "log10") +
-  theme_minimal() +
-  theme(legend.position = "none") +
-  scale_x_log10(
-     breaks = trans_breaks("log10", function(x) 10^x),
-     labels = trans_format("log10", math_format(10^.x))
-  ) +
-  labs(title = "Distribution of Haplotype Lengths by Sample", fill = "Haplotype Length (bp)") +
-  xlab("Haplotype Length (log scale)") +
-  ylab("")
-```
-
+## per sample
 ### stats per sample {.no-title}
 ```{r echo= FALSE, message = FALSE, warning = FALSE, out.width="100%"}
 persample <- df %>% group_by(sample) %>% summarise(
@@ -249,4 +235,21 @@ DT::datatable(
   colnames = c("Sample", "Haplotypes", "Mean SNPs", "Median SNPs", "Mean Haplotype Length", "Median Haplotype Length", "Largest Haplotype"),
   fillContainer = F
 )
-```
+```
+
+## ridgeplot
+### the ridgeplot {.no-title}
+```{r warning=FALSE, message=FALSE, echo= FALSE, fig.height=ridgeheight.samples, fig.width=8}
+ggplot(df, aes(x = block_length, y = sample, fill = stat(x))) +
+  geom_density_ridges_gradient(rel_min_height = 0.01) +
+  scale_fill_viridis_c(option = "G", trans = "log10") +
+  theme_minimal() +
+  theme(legend.position = "none") +
+  scale_x_log10(
+     breaks = trans_breaks("log10", function(x) 10^x),
+     labels = trans_format("log10", math_format(10^.x))
+  ) +
+  labs(title = "Distribution of Haplotype Lengths by Sample", fill = "Haplotype Length (bp)") +
+  xlab("Haplotype Length (log scale)") +
+  ylab("")
+```