Let’s view the data set

kable((Merkel))

We can now add color by Dose and a legend

col <- ifelse(Merkel$dose == 80, 
              "steelblue", # if dose = 80 mg, then the color will be steel blue
              "cadetblue") # if dose != 80 mg (i.e. 150 mg here), then the color will be cadet blue

MCC<- barplot(Merkel$response, 
              col=col, 
              border=col, 
              space=0.5, 
              ylim=c(-50,50),
              main = "Waterfall plot for Target Lesion Tumor Size", 
              ylab="Change from baseline (%)",
              cex.axis=1.5, 
              legend.text= c( "80mg", "150mg"),
              args.legend=list(title="Treatment Dose", fill=c("steelblue", "cadetblue"), border=NA, cex=0.9))

Or by disease type…

col <- ifelse(Merkel$type == "laMCC", 
              "#BC5A42", # if type of disease = locally MCC, then the color will be #BC5A42 (deep red)
              "#009296") # if type of disease != locaally MCC (i.e. mMCC), then the color will be ##009296 (greenish-blue)

MCC<- barplot(Merkel$response, 
              col=col, 
              border=col, 
              space=0.5, 
              ylim=c(-50,50),
              main = "Waterfall plot for Target Lesion Tumor Size", 
              ylab="Change from baseline (%)",
              cex.axis=1.5, 
              legend.text= c( "locally advanced MCC", "Metastatic MCC"),
              args.legend=list(title="Disease", fill=c("#BC5A42", "#009296"), border=NA, cex=0.9))

Or by Best overall response and provide a legend

col <- ifelse(Merkel$BOR == "CR", 
              "green", # if a subject had a CR the bar will be green, if they did not have a CR....
              ifelse(Merkel$BOR == "PR", 
                     "steelblue", # then, if a subject had a PR the bar will be steel blue, if they did not have a PR or CR....
                     ifelse(Merkel$BOR == "PD", 
                            "red", # then, if a subject had a PD the bar will be red, otherwise if they did not have a PR or CR or PD.... 
                            ifelse(Merkel$BOR == "SD", 
                                   "cadetblue", # then they must have ahd a SD, so the bar will be cadetblue, otherwise....
                                   "") # the color will be blank (which is not really an option, b/c they must have either a CR, PR, PD or SD)
                            )))

              
MCC<- barplot(Merkel$response, 
              col=col, 
              border=col, 
              space=0.5, 
              ylim=c(-50,50),
              main = "Waterfall plot for Target Lesion Tumor Size", ylab="Change from baseline (%)",
              cex.axis=1.5, 
              legend.text= c( "CR: Complete Response", "PR: Partial Response", "SD: Stable Disease", "PD: Progressive Disease"),
              args.legend=list(title="Best Overall Response", fill=c("green","steelblue",  "cadetblue", "red"), border=NA, cex=0.9))

Let’s add horizontal lines at 20% and -30%

• The majority of clinical trials use the Response Evaluation Criteria in Solid Tumors (RECIST) to assess tumor responses to a therapeutic intervention
  
• Per RECIST, tumor responses are adjudicated based on the following observations:
  • Complete Response (CR) Disappearance of all target lesions (sum of all taget lesions = 0)
    • Of note, any pathological lymph nodes (whether target or non-target) must have a reduction in size to < 10 mm
      
  • Partial Response (PR) >= 30% decrease (vs baseline) of sum of all target lesions dimension
    
  • Progressive Disease (PD) new lesions or >= 20% increase (vs smallest sum of target lesions or nadir)
    
  • Stable Disease (SD) when sum of all target lesions does not qualify for CR/PR/PD
    
• Thus, it is often useful to have lines to denote “Progressive Disease” and “Partial Response” on waterfall plots
  • Those bars between the PD and PR lines denote “Stable Disease”

col <- ifelse(Merkel$BOR == "CR", 
              "green",
              ifelse(Merkel$BOR == "PR", 
                     "steelblue",
                     ifelse(Merkel$BOR == "PD", 
                            "red", 
                            ifelse(Merkel$BOR == "SD", 
                                   "cadetblue", ""))))

MCC<- barplot(Merkel$response, 
              col=col, 
              border=col, 
              space=0.5, 
              ylim=c(-50,50),
              main = "Waterfall plot for Target Lesion Tumor Size",
              ylab="Change from baseline (%)",
              cex.axis=1.5, 
              legend.text= c( "CR: Complete Response", "PR: Partial Response", "SD: Stable Disease", "PD: Progressive Disease"),
              args.legend=list(title="Best Overall Response", fill=c("green","steelblue",  "cadetblue", "red"), border=NA, cex=1.0))

# Use the abline() function
## The abline() function is a simple way to add lines in R
### It takes the arguments: abline(a=NULL, b=NULL, h=NULL, v=NULL, ...)
#### a, b : single values denoting the intercept and the slope of the line
#### h : the y-value(s) for horizontal line(s)
#### v : the x-value(s) for vertical line(s)

abline(h=20, col = "black", lwd=0.5) # The "PD" line
abline(h=-30, col = "black", lwd=0.5) # This "PR" line