src/03_ERCC_analysis_code.R: fig size change

src/03_ERCC_analysis_code.R

@@ -56,7 +56,7 @@ corr_values <- tibble(
     )
 )
 
-pdf("./results/ERCC_analysis/Correlation_recap.pdf", width = 12, height = 100)
+pdf("./results/ERCC_analysis/Correlation_recap.pdf", width = 12, height = 8)
 ggplot(corr_values %>% arrange(group),
     mapping = aes(x = group, y = correlation)
 ) +
@@ -70,9 +70,9 @@ dev.off()
 ########################
 
 data_count_matrix <- get_count_matrix(
-    "data/09_htseq_count/with_unnmmaped", "BRAF|DMSO",
+    "data/09_htseq_count", "BRAF|DMSO",
     c("DMSO_0", "_T_"), "*_no_spike-in.tsv",
-    0, F
+    0, T
 )
 
 ercc_count_matrix <- get_count_matrix(
@@ -88,10 +88,12 @@ data_sample <- get_sample_count(data_count_matrix)
 ercc_sample <- get_sample_count(ercc_count_matrix)
 relative_counts <- get_relative_count(data_sample, ercc_sample)
 relative_counts <- relative_counts %>% arrange(name)
+pdf("./results/ERCC_analysis/ratio_ercc_on_genecount.pdf", 
+    width = 12, height = 8)
 ggplot(relative_counts, mapping = aes(x = name, y = relative_count)) +
-    geom_point() +
+    geom_boxplot() +
     theme(axis.text.x = element_text(angle = 90))
-
+dev.off()
 
 # Normalisation
 full_matrix <- rbind(data_count_matrix, ercc_count_matrix)