add text to plot or legend for second axis only R-CodePudding

I very nearly have the plot that I wan't so I think this will be an easy fix for someone more R savvy than myself

Sample_ID <- c("P1014B", "P1014F", "P1036A", "P1036B", "P1036C", "P1036D", "P1036E", "P1036F")
`CONTAMINATION_SCORE (NA)` <- c(2677, 1021, 870, 6831, 1324, 4175, 1370, 875)
`CONTAMINATION_P_VALUE (NA)` <- c(0.101, 1.000, 1.000, 0.000, 1.000, 0.036, 1.000, 1.000)
contam_reads <- data.frame(Sample_ID, `CONTAMINATION_SCORE (NA)`, `CONTAMINATION_P_VALUE (NA)`, check.names = FALSE)

I have a plot that is very near to what I want:

cols = c("P-value upper Limit" = "black","Contam. score upper limit" = "red")

ggplot(contam_reads[-c(1,2),], aes(x=Sample_ID, y=`CONTAMINATION_SCORE (NA)`))    
  geom_bar(stat="identity", fill="cyan4")  
  geom_hline(aes(yintercept=contam_reads$`CONTAMINATION_SCORE (NA)`[1]), col = cols[2], size = 1.5, linetype=2)  
  geom_hline(aes(yintercept=contam_reads$`CONTAMINATION_P_VALUE (NA)`[1]*10000), col = cols[1], size = 1, linetype=2)  
  geom_point(aes(x=Sample_ID, y=`CONTAMINATION_P_VALUE (NA)`* 10000),stat="identity",color="red", size = 1.5, show.legend = T)  
  labs(title= "DNA Library QC Metrics for Contamination",
       x="Sample ID",y="Contamination Score")  
  scale_y_continuous(sec.axis=sec_axis(~./10000,name="P-value", breaks = seq(0,1,0.1)))  
  theme(
    axis.title.y = element_text(color = "cyan4",size=15),
    axis.text.y = element_text(color = "cyan4"),
    axis.title.y.right = element_text(color = "red"),
    axis.text.y.right = element_text(color = "red")
  )      
  scale_colour_manual(values=cols)

I can't get the legend to be a line and not dots, and I can't get the first dot in the legend to turn black.

CodePudding user response：

You could fix your legend by mapping on aesthetics, i.e. instead of setting colors for the hlines as arguments map on the color aes and set show.legend=FALSE for geom_point to show just the lines. To this end I also use the data argument to pass just the first line of the dataset to the hlines.

Note 1: I added a named vector with labels for your scores and values. Also as names I use abbreviations for both the labels and color vector which makes it much easier to refer to a specific value in the ggplot code and makes the code easier to read.

Note 2: In my plot the colors for the lines are swapped which is right if p-values should be "red" and scores "black". Perhaps you confused that which could easily happen if one uses e.g. cols[1] to refer to colors.

cols <- c("pval" = "red", "score" = "black")
labels <- c("pval" = "P-value upper Limit", "score" = "Contam. score upper limit")

library(ggplot2)

ggplot(contam_reads[-c(1, 2), ], aes(x = Sample_ID, y = `CONTAMINATION_SCORE (NA)`))  
  geom_bar(stat = "identity", fill = "cyan4")  
  geom_hline(
    data = contam_reads[1, ],
    aes(yintercept = `CONTAMINATION_SCORE (NA)`, color = "score"),
    size = 1.5, linetype = 2
  )  
  geom_hline(
    data = contam_reads[1, ],
    aes(yintercept = `CONTAMINATION_P_VALUE (NA)` * 10000, color = "pval"),
    size = 1, linetype = 2
  )  
  geom_point(aes(x = Sample_ID, y = `CONTAMINATION_P_VALUE (NA)` * 10000, color = "pval"),
    stat = "identity", size = 1.5, show.legend = FALSE
  )  
  labs(
    title = "DNA Library QC Metrics for Contamination",
    x = "Sample ID", y = "Contamination Score",
    color = NULL
  )  
  scale_y_continuous(sec.axis = sec_axis(~ . / 10000, name = "P-value", breaks = seq(0, 1, 0.1)))  
  theme(
    axis.title.y = element_text(color = "cyan4", size = 15),
    axis.text.y = element_text(color = "cyan4"),
    axis.title.y.right = element_text(color = "red"),
    axis.text.y.right = element_text(color = "red")
  )  
  scale_colour_manual(values = cols, labels = labels)