Slope Chart - ggplot2

Question

I am testing some templates of ggplot2, and I am interesting to the slope chart, available from here:

Slope Chart - Link

It works perfectly.

I am only trying to make a similar one but with only a group defined, like the following code:

library(dplyr)
library(ggplot2)
theme_set(theme_classic())
source_df <- read.csv("https://raw.githubusercontent.com/jkeirstead/r-slopegraph/master/cancer_survival_rates.csv")

source_df <- filter(source_df, group == "Thyroid")

then I copy the remaining code from the example:

# Define functions. Source: https://github.com/jkeirstead/r-slopegraph
tufte_sort <- function(df, x="year", y="value", group="group", method="tufte", min.space=0.05) {
    ## First rename the columns for consistency
    ids <- match(c(x, y, group), names(df))
    df <- df[,ids]
    names(df) <- c("x", "y", "group")

    ## Expand grid to ensure every combination has a defined value
    tmp <- expand.grid(x=unique(df$x), group=unique(df$group))
    tmp <- merge(df, tmp, all.y=TRUE)
    df <- mutate(tmp, y=ifelse(is.na(y), 0, y))
  
    ## Cast into a matrix shape and arrange by first column
    require(reshape2)
    tmp <- dcast(df, group ~ x, value.var="y")
    ord <- order(tmp[,2])
    tmp <- tmp[ord,]
    
    min.space <- min.space*diff(range(tmp[,-1]))
    yshift <- numeric(nrow(tmp))
    ## Start at "bottom" row
    ## Repeat for rest of the rows until you hit the top
    for (i in 2:nrow(tmp)) {
        ## Shift subsequent row up by equal space so gap between
        ## two entries is >= minimum
        mat <- as.matrix(tmp[(i-1):i, -1])
        d.min <- min(diff(mat))
        yshift[i] <- ifelse(d.min < min.space, min.space - d.min, 0)
    }

    
    tmp <- cbind(tmp, yshift=cumsum(yshift))

    scale <- 1
    tmp <- melt(tmp, id=c("group", "yshift"), variable.name="x", value.name="y")
    ## Store these gaps in a separate variable so that they can be scaled ypos = a*yshift + y

    tmp <- transform(tmp, ypos=y + scale*yshift)
    return(tmp)
   
}

plot_slopegraph <- function(df) {
    ylabs <- subset(df, x==head(x,1))$group
    yvals <- subset(df, x==head(x,1))$ypos
    fontSize <- 3
    gg <- ggplot(df,aes(x=x,y=ypos)) +
        geom_line(aes(group=group),colour="grey80") +
        geom_point(colour="white",size=8) +
        geom_text(aes(label=y), size=fontSize, family="American Typewriter") +
        scale_y_continuous(name="", breaks=yvals, labels=ylabs)
    return(gg)
}    

## Prepare data    
df <- tufte_sort(source_df, 
                 x="year", 
                 y="value", 
                 group="group", 
                 method="tufte", 
                 min.space=0.05)

df <- transform(df, 
                x=factor(x, levels=c(5,10,15,20), 
                            labels=c("5 years","10 years","15 years","20 years")), 
                y=round(y))

## Plot
plot_slopegraph(df) + labs(title="Estimates of % survival rates") + 
                      theme(axis.title=element_blank(),
                            axis.ticks = element_blank(),
                            plot.title = element_text(hjust=0.5,
                                                      family = "American Typewriter",
                                                      face="bold"),
                            axis.text = element_text(family = "American Typewriter",
                                                     face="bold"))

The problem I find is that the connecting lines disappears if I take only one object in source_df$group ()in this case Thyroid, like the followings:

If I add only another item in the same column everything is fine and the connecting line appears.

Is there a way to have the lines also in this situation? I have tried on a lot of ways, removing the lines containing NA values without success, therefore I do not know how to fix this problem, if ... it is possible to be fixed.

Thank you in advance for every eventual reply!

Answer 1

May I suggest a much easier way, with the {ggh4x} package, which has a base R type = "b" like geom. You can remove the points, and plot text instead.

You'll get your result in three lines of code :)

library(tidyverse)
library(ggh4x)

source_df <- read.csv("https://raw.githubusercontent.com/jkeirstead/r-slopegraph/master/cancer_survival_rates.csv")
source_df <- filter(source_df, group == "Thyroid")

ggplot(source_df, aes(year, value)) +
## set shape to NA                
  geom_pointpath(aes(group = group, mult = 1), shape = NA)  +
  geom_text(aes(label = value))

^{Created on 2021-12-30 by the reprex package (v2.0.1)}

Answer 2

I fixed simply adding the line:

df <- df[complete.cases(df), ]

Before the graphing instructions. The problem was the generation of many lines with NA values and this line removes lines with null value.