fixes.

DESCRIPTION

@@ -27,6 +27,7 @@ Imports:
     optparse,
     reshape2,
     proto,
+    grid,
     ggplot2 (>= 1.0.1),
     RSQLite,
     logspline,

R/support-save_plots.R

@@ -10,6 +10,7 @@
 
 # Save the last ggplot() object created. For each output format,
 # generate a plot and put in the output directory
+
 #' @export
 save_plots <- function(
 	features_analysis,

inst/scripts/analysis/plots/antibodies/contacts/ag_ab_contact_den.R

@@ -58,7 +58,7 @@ run=function(self, sample_sources, output_dir, output_formats){
   p <- ggplot(data=binary_data, na.rm=T, aes(x=CDR)) +
     geom_bar(position="dodge", aes(y=percent, fill=sample_source), stat='identity') +
     ggtitle("CDR Makes Antigen Contact") +
-    scale_y_continuous(label=percent) +
+    scale_y_continuous(label="percent") +
     ylab("% of sample source")
   plot_field(p, "cdr_makes_contact_hist")
   save_tables(self, binary_data, "cdr_makes_contact_table", sample_sources, output_dir, output_formats,
@@ -117,7 +117,7 @@ run=function(self, sample_sources, output_dir, output_formats){
     ggtitle("Average Percent of total contacts") +
     xlab("CDR") +
     ylab("Avg %") +
-    scale_y_continuous(label=percent)
+    scale_y_continuous(label="percent")
   plot_field(p, "avg_perc_total_contacts_hist")
   save_tables(self, avg_perc, "avg_perc_total_contacts_table", sample_sources, output_dir, output_formats,
     caption="Avg Percent of total contacts", caption.placement="top", quote_strings=F)

inst/scripts/analysis/plots/interfaces/hbonds/int_hbonds_den.R

@@ -138,14 +138,14 @@ run=function(self, sample_sources, output_dir, output_formats){
   #Histogram
   p <- ggplot(data=hbond_counts, na.rm=T) + 
     geom_bar(aes(x=n, y = ..density.. , fill=sample_source), position="dodge", binwidth=1) +
-    scale_y_continuous(label=percent) +
+    scale_y_continuous(label="percent") +
     xlab("hbonds") +
     ggtitle("Average Cross Interface Hydrogen Bonds")
   plot_field(p, "hbond_hist_by_all")
 
   p <- ggplot(data=hbond_counts, na.rm=T) + 
     geom_bar(aes(x=n, y = ..density.. , fill=sample_source), position="dodge", binwidth=1) +
-    scale_y_continuous(label=percent) +
+    scale_y_continuous(label="percent") +
     xlab("hbonds") +
     ggtitle("Average Cross Interface Hydrogen Bonds")
   plot_field(p, "hbond_hist_by_interface", grid=~interface)

inst/scripts/analysis/plots/scores/total_score.R

@@ -10,6 +10,7 @@
 
 library(ggplot2)
 library(plyr)
+#library(grid)
 
 feature_analyses <- c(feature_analyses, methods::new("FeaturesAnalysis",
 id = "total_score",

install_local.R

@@ -2,9 +2,15 @@
 
 #NOTE: You must run this script with SUDO!!
 
-
 #install.packages("devtools", repos="http://cran.rstudio.com/")
+
+required_packages <- c("devtools", "roxygen2")
+
+if (length(setdiff(required_packages, rownames(installed.packages()))) > 0) {
+  install.packages(setdiff(required_packages, rownames(installed.packages())), repos="http://cran.rstudio.com/")  
+}
+
 devtools::document() # if you changed function signatures
 devtools:build()
 
-devtools::install_local(".")
+devtools::install_local(".")