Fixed alignment of x-axes, when they are at a 90 degree angle.

R/fit_to_signatures_strict.R

@@ -217,7 +217,7 @@ plot_sim_decay <- function(sims, removed_sigs, max_delta) {
                       guide = FALSE) +
     labs(x = "Removed signatures", 
          y = paste0("Cosine similarity (max delta: ", max_delta, ")")) +
-    theme(axis.text.x = element_text(angle = 90, size = 12), 
+    theme(axis.text.x = element_text(angle = 90, size = 10, hjust = 1, vjust = 0.5), 
           text = element_text(size = 12))
   return(fig)
 }

R/plot_192_profile.R

@@ -103,7 +103,7 @@ plot_192_profile <- function(mut_matrix, colors = NA, ymax = 0.2, condensed = FA
           axis.title.y = element_text(size = 12, vjust = 1),
           axis.text.y = element_text(size = 8),
           axis.title.x = element_text(size = 12),
-          axis.text.x = element_text(size = 5, angle = 90, vjust = 0.4),
+          axis.text.x = element_text(size = 5, angle = 90, vjust = 0.5),
           strip.text.x = element_text(size = 9),
           strip.text.y = element_text(size = 9),
           panel.grid.major.x = element_blank(),

R/plot_96_profile.R

@@ -97,7 +97,7 @@ plot_96_profile <- function(mut_matrix, colors = NA, ymax = 0.2, condensed = FAL
       axis.title.y = element_text(size = 12, vjust = 1),
       axis.text.y = element_text(size = 8),
       axis.title.x = element_text(size = 12),
-      axis.text.x = element_text(size = 5, angle = 90, vjust = 0.4),
+      axis.text.x = element_text(size = 5, angle = 90, vjust = 0.5),
       strip.text.x = element_text(size = 9),
       strip.text.y = element_text(size = 9),
       panel.grid.major.x = element_blank(),

R/plot_bootstrapped_contribution.R

@@ -86,7 +86,7 @@ plot_bootstrapped_contribution <- function(contri_boots,
     labs(x = "Signature", y = ylab_text) +
     theme_classic() +
     theme(
-      axis.text.x = element_text(angle = 90, size = 10),
+      axis.text.x = element_text(angle = 90, size = 10, hjust = 1, vjust = 0.5),
       text = element_text(size = 12),
       strip.text.y = element_text(size = 8)
     )

R/plot_compare_dbs.R

@@ -115,7 +115,7 @@ plot_compare_dbs <- function(profile1, profile2,
     theme(
       panel.grid.major.x = element_blank(),
       strip.background = element_rect(fill = "cadetblue"),
-      axis.text.x = element_text(angle = 90)
+      axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)
     )
   return(fig)
 }

R/plot_compare_profiles.R

@@ -133,7 +133,7 @@ plot_compare_profiles <- function(profile1,
       axis.title.y = element_text(size = 12, vjust = 1),
       axis.text.y = element_text(size = 8),
       axis.title.x = element_text(size = 12),
-      axis.text.x = element_text(size = 5, angle = 90, vjust = 0.4),
+      axis.text.x = element_text(size = 5, angle = 90, vjust = 0.5),
       strip.text.x = element_text(size = 14),
       strip.text.y = element_text(size = 14),
       panel.grid.major.x = element_blank(),

R/plot_contribution_heatmap.R

@@ -165,7 +165,7 @@ plot_contribution_heatmap <- function(contribution, sig_order = NA, sample_order
     geom_raster() +
     scale_fill_distiller(palette = "YlGnBu", direction = 1, name = "Relative \ncontribution", limits = c(0, 1)) +
     theme_bw() +
-    theme(axis.text.x = element_text(angle = 90, hjust = 1)) +
+    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)) +
     labs(x = NULL, y = NULL)
   # if plot_values is TRUE, add values to heatmap
   if (plot_values) {

R/plot_correlation_bootstrap.R

@@ -28,6 +28,7 @@
 #'
 #' ## You can also look at the correlation for all samples combined
 #' plot_correlation_bootstrap(contri_boots, per_sample = FALSE)
+#' 
 plot_correlation_bootstrap <- function(contri_boots, per_sample = TRUE) {
 
   # These variables use non standard evaluation.
@@ -109,7 +110,7 @@ plot_correlation_bootstrap_sample <- function(contri_boots, sample) {
     labs(x = NULL, y = NULL, title = sample) +
     theme_classic() +
     theme(
-      axis.text.x = element_text(angle = 90, hjust = 1),
+      axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5),
       text = element_text(size = 12),
       panel.border = element_rect(colour = "black", fill = NA, size = 1)
     )

R/plot_cosine_heatmap.R

@@ -168,7 +168,7 @@ plot_cosine_heatmap <- function(cos_sim_matrix, col_order = NA, row_order = NA,
     geom_raster() +
     scale_fill_distiller(palette = "YlGnBu", direction = 1, name = "Cosine \nsimilarity", limits = c(0, 1.000000001)) +
     theme_bw() +
-    theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
+    theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5, size = 8)) +
     labs(x = NULL, y = NULL)
 
   # if plot_values is TRUE, add values to heatmap

R/plot_dbs_contexts.R

@@ -88,7 +88,7 @@ plot_dbs_contexts <- function(counts, same_y = FALSE) {
     theme(
       panel.grid.major.x = element_blank(),
       strip.background = element_rect(fill = "cadetblue"),
-      axis.text.x = element_text(angle = 90)
+      axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)
     )
 
   return(fig)

R/plot_lesion_segregation.R

@@ -158,7 +158,7 @@ plot_lesion_segregation_gg <- function(tb, tb_limits, x_axis_breaks, point_size,
     theme_bw() +
     theme(
       text = element_text(size = 18),
-      axis.text.x = element_text(size = 11, angle = 90),
+      axis.text.x = element_text(size = 11, angle = 90, vjust = 0.5, hjust = 1),
       axis.text.y = element_text(size = 20),
       panel.grid.minor = element_blank()
     )

R/plot_long_profile.R

@@ -112,7 +112,7 @@ plot_long_profile <- function(mut_matrix, mode = c("relative_sample", "relative_
           axis.title.y = element_text(size = 12, vjust = 1),
           axis.text.y = element_text(size = 8),
           axis.title.x = element_text(size = 12),
-          axis.text.x = element_text(size = 5, angle = 90, vjust = 0.4),
+          axis.text.x = element_text(size = 5, angle = 90, vjust = 0.5),
           strip.text.x = element_text(size = 9),
           strip.text.y = element_text(size = 9),
           panel.grid.major.x = element_blank(),

R/plot_main_dbs_contexts.R

@@ -78,7 +78,7 @@ plot_main_dbs_contexts <- function(counts, same_y = FALSE) {
     theme_minimal() +
     theme(
       panel.grid.major.x = element_blank(),
-      axis.text.x = element_text(angle = 90)
+      axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)
     )
   return(fig)
 }

R/plot_main_indel_contexts.R

@@ -85,7 +85,7 @@ plot_main_indel_contexts <- function(counts, same_y = FALSE) {
     theme_minimal() +
     theme(
       panel.grid.major.x = element_blank(),
-      axis.text.x = element_text(angle = 90)
+      axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)
     )
   return(fig)
 }

R/plot_original_vs_reconstructed.R

@@ -61,7 +61,7 @@ plot_original_vs_reconstructed <- function(mut_matrix, reconstructed, y_intercep
     theme_classic() +
     theme(
       text = element_text(size = 12),
-      axis.text.x = element_text(angle = 90)
+      axis.text.x = element_text(angle = 90, hjust = 1, vjust = 0.5)
     )
   return(plot)
 }