Skipping NA values for a multiple line plot using GGplot (and combined with another plot using grid arrange)

Question

I am trying to skip NA values on a graph with two lines on it (ad13com & Pd13c), and combining it with a second graph (xPDd13C) using grid arrange. Using my code, the line breaks due to NA values in my data and I am looking for continuous lines (three separate ones). I have tried using na.rm arguments but didn't make any progress as I'm quite new to r. I realise that the issue is coming from the fact that I am plotting the ungathered data but I don't know how to apply a skip NA argument to data thats being plotted this way!

In my code, I first gather the data before plotting it as I am using a similar script for when I produced multiple plots using facet wrap, so it may not be necessary to gather the data for this application? I also realise I have multiple y axis scales so it just replaces the existing scale and uses the last one, I wasn't too sure how to remove it properly so I just left it in as it works fine

Anyway here is my code:

theme_set(theme_paleo(8))
theme_update(plot.title = element_text(hjust = 0.5))

#read the data
data <- read_csv("profundal.csv", col_types = cols(.default = col_guess())
)

#first gather the data and set out the omit na function in order to skip na values
data %>% filter(core_id == "BKM0817") %>%
  gather(key = param, value = value, -core_id, -Age, -depth) %>% 
  na.omit()

#plot the first graph
prof1 <- 
  ggplot() +
  geom_lineh(data = data, mapping = aes(x=ad13com, y = Age), colour = "black", size = 1) +
  geom_point(data = data, mapping = aes(x=ad13com, y = Age), colour = "black", size = 2) +
  geom_lineh(data = data, mapping = aes(x=Pd13c, y = Age), linetype = 2, colour = "black", size = 1,) +
  geom_point(data = data, mapping = aes(x=Pd13c, y = Age), shape=0, colour = "black", size = 2.7) +
  scale_y_reverse() +
  labs (x = expression(delta ^13*"C (\u2030 V-PDB)"), y = "Age (Cal. yrs BP)") +
  ggtitle(expression(delta ^13*"C"[OM]~"and Chironomus")) +
  theme(panel.border = element_blank(), panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))

#plot the second graph
prof2 <- 
  ggplot() +
  geom_lineh(data = data, mapping = aes(x=xPDd13C, y = Age), colour = "black", size = 1) +
  geom_point(data = data, mapping = aes(x=xPDd13C, y = Age), shape = 2, colour = "black", size = 2) +
  scale_y_reverse(# Features of the first axis
    name = "Age (Cal. yrs BP)",
    
    # Add a second axis and specify its features
    sec.axis = sec_axis( trans=~./17.927, name="Depth (cm)")
  ) +
  labs(x = expression(delta ^13*"C (\u2030 V-PDB)"), y = "Age (Cal. yrs BP)") +
  ggtitle( expression(Delta*delta ^13*"C")) +
  theme(panel.border = element_blank(), panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))

#combine the plots
profundal <-gridExtra::grid.arrange(
  prof1,
  prof2 + 
    labs(y = NULL) +
    scale_y_reverse(labels = NULL, name = "Age (Cal. yrs BP)",
                    
                    # Add a second axis and specify its features
                    sec.axis = sec_axis( trans=~./17.927, name="Depth (cm)")) +
    theme(
      plot.margin = unit(c(0.05,0.1, 0.056,0), "inches"),
      axis.ticks.y = element_blank(),
      plot.background = element_blank()
    ),
  nrow = 1,
  widths = c(4, 4)
)

# save the file 
ggsave("test.png", units="in", width=8, height=6, dpi=300, plot=profundal)

Many thanks in advance!

Answer 1

Where you have used na_omit() on data the results are not assigned to anything. You need to assign the results to data (or something else).

data <- data %>% filter(core_id == "BKM0817") %>%
  gather(key = param, value = value, -core_id, -Age, -depth) %>% 
  na.omit()

Answer 2

I managed to plot the new data after it was gathered (as Tjn suggested with the na.omit function at the end) like this.

data2 <- data %>% filter(core_id == "BKM0817") %>%
  gather(key = param, value = value, -core_id, -Age, -depth) %>% 
  na.omit()

The data then looks like this:

In order to plot two lines on the same graph, I then had to subset the data and plot the lines and points individually like this for the first graph and follows the same structure for the second graph:

prof1 <-
  ggplot() +
  geom_lineh(data = subset(data2,param %in% "ad13com"), mapping = aes(x=value, y = Age), colour = "black", size = 1) +
  geom_point(data = subset(data2,param %in%"ad13com"), mapping = aes(x=value, y = Age), colour = "black", size = 2) +
  geom_lineh(data = subset(data2,param %in% "Pd13c"), mapping = aes(x=value, y = Age), linetype = 2, colour = "black", size = 1,) +
  geom_point(data = subset(data2,param %in% "Pd13c"), mapping = aes(x=value, y = Age), shape=0, colour = "black", size = 2.7) +
  scale_y_reverse() +
  labs (x = expression(delta ^13*"C (\u2030 V-PDB)"), y = "Age (Cal. yrs BP)") +
  ggtitle(expression(delta ^13*"C"[OM]~"and Chironomus")) +
  theme(panel.border = element_blank(), panel.grid.major = element_blank(),
        panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))

The final result is now the same as the graph in the question but now with lines linking all the points individually.