create line plot of RFU distribution across groups at different timepoints

linepoint_with_stats.R

# from http://www.sthda.com/english/wiki/ggplot2-line-plot-quick-start-guide-r-software-and-data-visualization
#+++++++++++++++++++++++++
# Function to calculate the mean and the standard deviation
  # for each group
#+++++++++++++++++++++++++
# data : a data frame
# varname : the name of a column containing the variable
  #to be summariezed
# groupnames : vector of column names to be used as
  # grouping variables
data_summary <- function(data, varname, groupnames){
  require(plyr)
  summary_func <- function(x, col){
    c(mean = mean(x[[col]], na.rm=TRUE),
      sd = sd(x[[col]], na.rm=TRUE))
  }
  data_sum<-ddply(data, groupnames, .fun=summary_func,
                  varname)
  data_sum <- rename(data_sum, c("mean" = varname))
 return(data_sum)
}
# generate mean and sd by group
test_table_stats <- data_summary(
  test_table, 
  varname="q_norm", 
  groupnames = c("rash_level", "timepoint")
  )
# Use position_dodge to move overlapped errorbars horizontally
ggplot(
  test_table_stats, 
  aes(x=timepoint, 
      y=q_norm, 
      group=rash_level, 
      color=rash_level)
  ) + 
  geom_errorbar(aes(ymin=q_norm-sd, ymax=q_norm+sd), width=.1, 
  position=position_dodge(0.05)) +
  geom_line() + 
  geom_point()+
  scale_color_manual(values = c("None" = "grey", "Grade1" = "orange", "Grade2" = "red")) + 
  theme_minimal() +
  ggplot2::ylab("RFU") +
  ggplot2::ggtitle("test")