Add plot saving examples (#202)

README.Rmd

@@ -172,9 +172,17 @@ gg_list <- visualize_terms(
  input_processed = input_processed,
  is_KEGG_result = TRUE
 ) # this function returns a list of ggraph objects (named by Term ID)
+
+# save one of the plots as PDF image
+ggplot2::ggsave(
+ "hsa04911_diagram.pdf", # path to output, format is determined by extension
+ gg_list$hsa04911, # what to plot
+ width = 5 # adjust width
+ height = 5 # adjust height
+) 
 ```
 
-![KEGG Pathway Diagram](https://github.com/egeulgen/pathfindR/blob/master/vignettes/example_kegg_pathway_diagram.png?raw=true "KEGG Pathway Diagram")
+![KEGG Pathway Diagram](https://github.com/egeulgen/pathfindR/blob/master/vignettes/example_kegg_pathway_diagram.png?raw=true)
 
 Alternatively (i.e., for other types of (non-KEGG) enrichment analyses), an interaction diagram per enriched term can be generated again via `visualize_terms()`. These diagrams are also returned as `ggraph` objects:
 
@@ -186,9 +194,17 @@ gg_list <- visualize_terms(
  is_KEGG_result = FALSE,
  pin_name_path = "Biogrid"
 ) # this function returns a list of ggraph objects (named by Term ID)
+
+# save one of the plots as PDF image
+ggplot2::ggsave(
+ "diabetic_cardiomyopathy_interactions.pdf", # path to output, format is determined by extension
+ gg_list$hsa04911, # what to plot
+ width = 10 # adjust width
+ height = 6 # adjust height
+) 
 ```
 
-![Interaction Diagram](https://github.com/egeulgen/pathfindR/blob/master/vignettes/example_interaction_vis.png?raw=true "Interaction Diagram")
+![Interaction Diagram](https://github.com/egeulgen/pathfindR/blob/master/vignettes/example_interaction_vis.png?raw=true)
 
 ## Term-Gene Heatmap
 

README.md

@@ -230,12 +230,20 @@ gg_list <- visualize_terms(
  input_processed = input_processed,
  is_KEGG_result = TRUE
 ) # this function returns a list of ggraph objects (named by Term ID)
+
+# save one of the plots as PDF image
+ggplot2::ggsave(
+ "hsa04911_diagram.pdf", # path to output, format is determined by extension
+ gg_list$hsa04911, # what to plot
+ width = 5 # adjust width
+ height = 5 # adjust height
+) 
 ```
 
 <figure>
 <img
 src="https://github.com/egeulgen/pathfindR/blob/master/vignettes/example_kegg_pathway_diagram.png?raw=true"
-title="KEGG Pathway Diagram" alt="KEGG Pathway Diagram" />
+alt="KEGG Pathway Diagram" />
 <figcaption aria-hidden="true">KEGG Pathway Diagram</figcaption>
 </figure>
 
@@ -252,12 +260,20 @@ gg_list <- visualize_terms(
  is_KEGG_result = FALSE,
  pin_name_path = "Biogrid"
 ) # this function returns a list of ggraph objects (named by Term ID)
+
+# save one of the plots as PDF image
+ggplot2::ggsave(
+ "diabetic_cardiomyopathy_interactions.pdf", # path to output, format is determined by extension
+ gg_list$hsa04911, # what to plot
+ width = 10 # adjust width
+ height = 6 # adjust height
+) 
 ```
 
 <figure>
 <img
 src="https://github.com/egeulgen/pathfindR/blob/master/vignettes/example_interaction_vis.png?raw=true"
-title="Interaction Diagram" alt="Interaction Diagram" />
+alt="Interaction Diagram" />
 <figcaption aria-hidden="true">Interaction Diagram</figcaption>
 </figure>
 

vignettes/intro_vignette.Rmd

@@ -231,11 +231,19 @@ For KEGG enrichment analyses, `visualize_terms()` can be used to generate KEGG p
 
 ```{r KEGG_vis, eval=FALSE}
 input_processed <- input_processing(example_pathfindR_input)
-visualize_terms(
+gg_list <- visualize_terms(
  result_df = example_pathfindR_output,
  input_processed = input_processed,
  is_KEGG_result = TRUE
 ) # this function returns a list of ggraph objects (named by Term ID)
+
+# save one of the plots as PDF image
+ggplot2::ggsave(
+ "hsa04911_diagram.pdf", # path to output, format is determined by extension
+ gg_list$hsa04911, # what to plot
+ width = 5 # adjust width
+ height = 5 # adjust height
+) 
 ```
 
 <img src="./example_kegg_pathway_diagram.png" style="max-width:100%;" />
@@ -244,12 +252,20 @@ Alternatively (i.e., for other types of non-KEGG enrichment analyses), an intera
 
 ```{r nonKEGG_viss, eval=FALSE}
 input_processed <- input_processing(example_pathfindR_input)
-visualize_terms(
+gg_list <- visualize_terms(
  result_df = example_pathfindR_output,
  input_processed = input_processed,
  is_KEGG_result = FALSE,
  pin_name_path = "Biogrid"
 ) # this function returns a list of ggraph objects (named by Term ID)
+
+# save one of the plots as PDF image
+ggplot2::ggsave(
+ "diabetic_cardiomyopathy_interactions.pdf", # path to output, format is determined by extension
+ gg_list$hsa04911, # what to plot
+ width = 10 # adjust width
+ height = 6 # adjust height
+) 
 ```
 
 <img src="./example_interaction_vis.png" style="max-width:100%;" />

vignettes/visualization_vignette.Rmd

@@ -55,11 +55,19 @@ For KEGG enrichment analyses, `visualize_terms()` can be used to generate KEGG p
 
 ```{r KEGG_vis, eval=FALSE}
 input_processed <- input_processing(example_pathfindR_input)
-visualize_terms(
+gg_list <- visualize_terms(
  result_df = example_pathfindR_output,
  input_processed = input_processed,
  is_KEGG_result = TRUE
 ) # this function returns a list of ggraph objects (named by Term ID)
+
+# save one of the plots as PDF image
+ggplot2::ggsave(
+ "hsa04911_diagram.pdf", # path to output, format is determined by extension
+ gg_list$hsa04911, # what to plot
+ width = 5 # adjust width
+ height = 5 # adjust height
+) 
 ```
 
 <img src="./example_kegg_pathway_diagram.png" style="max-width:100%;" />
@@ -68,12 +76,20 @@ Alternatively (i.e., for other types of non-KEGG enrichment analyses), an intera
 
 ```{r nonKEGG_viss, eval=FALSE}
 input_processed <- input_processing(example_pathfindR_input)
-visualize_terms(
+gg_list <- visualize_terms(
  result_df = example_pathfindR_output,
  input_processed = input_processed,
  is_KEGG_result = FALSE,
  pin_name_path = "Biogrid"
 ) # this function returns a list of ggraph objects (named by Term ID)
+
+# save one of the plots as PDF image
+ggplot2::ggsave(
+ "diabetic_cardiomyopathy_interactions.pdf", # path to output, format is determined by extension
+ gg_list$hsa04911, # what to plot
+ width = 10 # adjust width
+ height = 6 # adjust height
+) 
 ```
 
 <img src="./example_interaction_vis.png" style="max-width:100%;" />