Merge pull request #8 from weaversd/master

v0.1.10

Author: weaversd

Documentation/Release Updates.txt

@@ -43,4 +43,9 @@ Version 0.1.9
 2022-11-18
  - Refactored tabs for streamlined use. Only one sample, two sample, and multiple sample are options now.
   - Other options are still available in drop down menus or in the sidebar
- - Rewrote documentation to reflect changes
+ - Rewrote documentation to reflect changes
+ 
+Version 0.1.10
+2022-11-22
+ - Increased all font sizes in plots
+ - updated required packages

Documentation/annotation_1.png

@@ -38,3 +38,9 @@ Alternative Method to run locally:
 
 
 Errors that occur when trying to run the app locally are almost always due to old versons of R, or the installed packages. To troubleshoot, install the most recent version of R, as well as the most recent version of all the packages referenced above.
+
+PrIntMap-R has been tested and optimized on Windows and MacOS. The app also runs on linux, although it has not been optimized. Some versions of linux may open a new tab every time a plot is updated, making use impractical. If you experience this, try one of the following solutions:  
+
+  * Run PrIntMap-R on the online version
+  * Run PrIntMap-R on Windows or MacOS
+  * Run PrIntMap-R using Ubuntu locally on a virtual machine

Documentation/annotation_2.png

@@ -17,9 +17,9 @@ library(shinyjs)
 
 
 #reactlog
- library(reactlog)
- reactlog_enable()
- options(shiny.reactlog = TRUE)
+ #library(reactlog)
+ #reactlog_enable()
+ #options(shiny.reactlog = TRUE)
 
 #source functions and libraries
 source("www/libraries.R")

README.md

@@ -2,7 +2,7 @@ library(shiny)
 ui <- navbarPage(title = "PrIntMap-R",
                  tabPanel("Documentation",
                           includeMarkdown("Documentation/Documentation.md"),
-                          "Version 0.1.9"), #update version here for each push
+                          "Version 0.1.10"), #update version here for each push
                  tabPanel("Run",
                           flowLayout(
                             fileInput(inputId = "database_file", label = "Upload fasta database file",

global.R

@@ -506,7 +506,7 @@ create_volcano_plot <- function(df, fdr = 0.05,
                               p_val = p_val,
                               fold_change_category = fold_change_category)) +
 
-    theme_bw(base_size = 10) +
+    theme_bw(base_size = 15) +
     theme(panel.grid = element_blank(), legend.position = "none") +
     labs(x = (paste("Log2 fold-change: (", sample2, "/", sample1, ")",sep="")),
          y = "-Log10 (p-value)",

ui.R

@@ -579,7 +579,7 @@ combine_AA_intensity <- function(AA_df, intensity_vec) {
 #create simple plot
 #returns plot object
 plot_intensity <- function(AA_df, protein, intensity_label = "PSM",
-                           font_size = 15,color = "grey18",
+                           font_size = 18,color = "grey18",
                            alpha = 1, plot_type = "line") {
   if (plot_type == "bar") {
     plot <- ggplot(data = AA_df) +
@@ -664,7 +664,7 @@ add_origin_peptide_vector <- function(AA_df,
 #plot origin plot
 plot_origin <- function(AA_df, protein,
                         intensity_label = "PSM",
-                        font_size = 15, 
+                        font_size = 18, 
                         color = "grey18", alpha = 1, plot_type = "line") {
   if (plot_type == "bar") {
     plot <- ggplot(data = AA_df) +

www/Volcano_plot_functions.R

@@ -1,5 +1,5 @@
 plot_difference_comb_mult <- function(AA_df, protein, intensity_label = "PSM",
-                                 font_size = 15,
+                                 font_size = 18,
                                  alpha = 1, plot_type = "line") {
   plot <- ggplot(data = AA_df) +
     geom_hline(yintercept = 0, color = "red", size = 0.1, linetype = "dashed") +
@@ -15,7 +15,7 @@ plot_difference_comb_mult <- function(AA_df, protein, intensity_label = "PSM",
 }
 
 plot_foldchange_comb_mult <- function(AA_df, protein, intensity_label = "PSM",
-                                 font_size = 15,
+                                 font_size = 18,
                                  alpha = 1, plot_type = "line") {
   plot <- ggplot(data = AA_df) +
     geom_hline(yintercept = 1, color = "red", size = 0.1, linetype = "dashed") +

www/basic_functions.R

@@ -54,7 +54,7 @@ create_stacked_line_plot_yval <- function(peptide_dataframe, protein_name, prote
     geom_segment(aes(y = y_val, x = start, xend = end, yend = y_val,
                      color = intensity_value, length = length, peptide = peptide),
                  size = 1, lineend = "round") +
-    theme_bw(base_size = 15) +
+    theme_bw(base_size = 18) +
     theme(panel.grid = element_blank(),
           legend.position = "right",
           axis.text.y = element_blank(),
@@ -73,7 +73,7 @@ create_stacked_line_plot_intensity <- function(peptide_dataframe, protein_name,
     geom_segment(aes(y = intensity_value, x = start, xend = end, yend = intensity_value,
                      color = intensity_value, length = length, peptide = peptide),
                  size = 1, lineend = "round") +
-    theme_bw(base_size = 15) +
+    theme_bw(base_size = 18) +
     theme(panel.grid = element_blank(),
           legend.position = "right") +
     labs(x = "Amino Acid Position", y = intensity_label,