updates plots

CambridgeCentreForProteomics · Mar 11, 2020 · 154cece · 154cece
1 parent 952cfe1
commit 154cece
Show file tree

Hide file tree

Showing 15 changed files with 45 additions and 20 deletions.
diff --git a/README.md b/README.md
@@ -2,14 +2,17 @@
 
 This repository was used to generate figures for the OOPS Nature Protocols manuscript
 
+Additionally, a tutorial for identifying changes in RNA binding using OOPS is provided:
+('Identify_changes_in_RNA_binding.Rmd')
+
 The repository structure is:
 
 - raw:
-Copies of supplementary data from the original OOPS publication (https://www.nature.com/articles/s41587-018-0001-2)
+  Copies of supplementary data from the original OOPS publication (https://www.nature.com/articles/s41587-018-0001-2)
 
 - notebooks:
-R markdown notebooks to analyse data and generate figures
+  R markdown notebooks
 
 - results/plots:
-Plots from notebooks
+  Plots from notebooks
 
diff --git a/notebooks/Identify_changes_in_RNA_binding.Rmd b/notebooks/Identify_changes_in_RNA_binding.Rmd
@@ -273,6 +273,7 @@ p <- limma_results %>%
   
 print(p)
 ggsave('../results/plots/rna_binding_changes_volcano.png')
+ggsave('../results/plots/rna_binding_changes_volcano.pdf')
 ```
 
 

diff --git a/notebooks/Identify_changes_in_RNA_binding.nb.html b/notebooks/Identify_changes_in_RNA_binding.nb.html
diff --git a/notebooks/Identify_changes_in_RNA_binding.pdf b/notebooks/Identify_changes_in_RNA_binding.pdf
diff --git a/notebooks/OOPS_CL_RNase_control_ratios.Rmd b/notebooks/OOPS_CL_RNase_control_ratios.Rmd
@@ -78,6 +78,7 @@ ratios_p1 <- combined_cl_rnase %>%
 
 print(ratios_p1)
 ggsave('../results/plots/ratios_p1.png')
+ggsave('../results/plots/ratios_p1.pdf')
 
 ratios_p2 <- combined_cl_rnase %>% 
   mutate(exp=factor(exp, levels=c('RNase:Ctrl', 'CL:NC'))) %>%
@@ -91,6 +92,7 @@ ratios_p2 <- combined_cl_rnase %>%
 
 print(ratios_p2)
 ggsave('../results/plots/ratios_p2.png')
+ggsave('../results/plots/ratios_p2.pdf')
 
 ```
 
diff --git a/notebooks/OOPS_CL_RNase_control_ratios.nb.html b/notebooks/OOPS_CL_RNase_control_ratios.nb.html
diff --git a/notebooks/OOPS_CL_RNase_control_ratios.pdf b/notebooks/OOPS_CL_RNase_control_ratios.pdf
diff --git a/notebooks/Visualise_dynamics.Rmd b/notebooks/Visualise_dynamics.Rmd
@@ -89,10 +89,11 @@ p <- glycolysis_intensities %>%
   geom_vline(xintercept=3.5) +
   geom_vline(xintercept=6.5) +
   scale_fill_gradient(low=cbPalette[1], high=cbPalette[5], name='Protein abundance\n(centre-median normalised)') +
-  theme(axis.text.y=element_text(size=10))
+  theme(axis.text.y=element_text(size=10), legend.title=element_text(size=10), legend.text=element_text(size=10))
 
 print(p)
 
-ggsave('../results/plots/rna_binding_changes_heatmap.png')
+ggsave('../results/plots/rna_binding_changes_heatmap.png', width=10, height=5)
+ggsave('../results/plots/rna_binding_changes_heatmap.pdf', width=10, height=5)
 ```
 
diff --git a/notebooks/Visualise_dynamics.nb.html b/notebooks/Visualise_dynamics.nb.html
diff --git a/notebooks/Visualise_dynamics.pdf b/notebooks/Visualise_dynamics.pdf
diff --git a/results/plots/ratios_p1.pdf b/results/plots/ratios_p1.pdf
diff --git a/results/plots/ratios_p2.pdf b/results/plots/ratios_p2.pdf
diff --git a/results/plots/rna_binding_changes_heatmap.pdf b/results/plots/rna_binding_changes_heatmap.pdf
diff --git a/results/plots/rna_binding_changes_heatmap.png b/results/plots/rna_binding_changes_heatmap.png
diff --git a/results/plots/rna_binding_changes_volcano.pdf b/results/plots/rna_binding_changes_volcano.pdf
-Original file line number
+Diff line change
@@ Expand Up / @@ -273,6 +273,7 @@ p <- limma_results %>% @@
     print(p)
     ggsave('../results/plots/rna_binding_changes_volcano.png')
+    ggsave('../results/plots/rna_binding_changes_volcano.pdf')
     ```
@@ Expand Down @@