问题

I'm trying to edit the labels in the legend so that the first label (WT) is in plain text, whilst the subsequent 7 are in italics. I have been using element_text(face=c("plain", rep("italic",7))) , but this has resulted in none of the labels being converted to italics. I'm a bit confused why it hasn't worked because element_text(face="italic") converts all the labels into italics. My plot is as follows:

library(tidyverse)

for_plot <- read_csv(file =
"Row, Time, Mutant, Mean
1, 1, ppi1, 0.8008
2, 1, sp1-1, 0.8038
3, 1, sp1-1 ppi1, 0.8094
4, 1, sp1-2 ppi1, 0.8138
5, 1, sp1-3 ppi1, 0.8066667
6, 1, sp1-4 ppi1, 0.7998
7, 1, sp1-5 ppi1, 0.8026667
8, 1, Wt, 0.8083333
9,  21, ppi1, 0.6806
10, 21, sp1-1, 0.7088
11, 21, sp1-1 ppi1, 0.6982
12, 21, sp1-2 ppi1, 0.7126
13, 21, sp1-3 ppi1, 0.709
14, 21, sp1-4 ppi1, 0.6942
15, 21, sp1-5 ppi1, 0.7096667
16, 21, Wt, 0.7246667
17, 56, ppi1, 0.6652
18, 56, sp1-1, 0.6848
19, 56, sp1-1 ppi1, 0.6816
20, 56, sp1-2 ppi1, 0.6926
21, 56, sp1-3 ppi1, 0.6945
22, 56, sp1-4 ppi1, 0.676
23, 56, sp1-5 ppi1, 0.6931667
24, 56, Wt, 0.6946667
25, 111, ppi1, 0.653
26, 111, sp1-1, 0.6704
27, 111, sp1-1 ppi1, 0.6704
28, 111, sp1-2 ppi1, 0.6756
29, 111, sp1-3 ppi1, 0.679
30, 111, sp1-4 ppi1, 0.664
31, 111, sp1-5 ppi1, 0.6805
32, 111, Wt, 0.677
33, 186, ppi1, 0.6132
34, 186, sp1-1, 0.633
35, 186, sp1-1 ppi1, 0.6298
36, 186, sp1-2 ppi1, 0.6402
37, 186, sp1-3 ppi1, 0.6435
38, 186, sp1-4 ppi1, 0.6278
39, 186, sp1-5 ppi1, 0.6478333
40, 186, Wt, 0.6403333
41, 281, ppi1, 0.5636
42, 281, sp1-1, 0.587
43, 281, sp1-1 ppi1, 0.5828
44, 281, sp1-2 ppi1, 0.5906
45, 281, sp1-3 ppi1, 0.5968333
46, 281, sp1-4 ppi1, 0.5838
47, 281, sp1-5 ppi1, 0.5983333
48, 281, Wt, 0.5948333")

for_plot %>%
 ggplot()+
  geom_line(aes(x = Time, y = Mean, col = Mutant)) +
  geom_point(aes(x = Time, y = Mean, col = Mutant)) + 
  labs(title = "Effective PSII Quantum Yield across SP1 Mutants", 
       y = "Effective PSII Quantum Yield",
       x = "Actinic PPFD") +
  theme(plot.title = element_text(hjust = 0.5)) +
  theme(legend.text = element_text(face=c("plain", rep("italic",7))))

^{Created on 2020-01-01 by the reprex package (v0.3.0)}

回答1:

I wrote the ggtext package to make these types of problems easier to solve. It allows you to style with markdown, i.e., just enclose the italics parts in stars.

The package is currently under development and needs to be installed via remotes, but it will be released on CRAN soon (spring 2020). You may also need the latest development version of ggplot2, which you can install via remotes::install_github("tidyverse/ggplot2").

library(tidyverse)
library(ggtext)  # remotes::install_github("clauswilke/ggtext")

for_plot <- read_csv(file =
"Row, Time, Mutant, Mean
1, 1, ppi1, 0.8008
2, 1, sp1-1, 0.8038
3, 1, sp1-1 ppi1, 0.8094
4, 1, sp1-2 ppi1, 0.8138
5, 1, sp1-3 ppi1, 0.8066667
6, 1, sp1-4 ppi1, 0.7998
7, 1, sp1-5 ppi1, 0.8026667
8, 1, Wt, 0.8083333
9,  21, ppi1, 0.6806
10, 21, sp1-1, 0.7088
11, 21, sp1-1 ppi1, 0.6982
12, 21, sp1-2 ppi1, 0.7126
13, 21, sp1-3 ppi1, 0.709
14, 21, sp1-4 ppi1, 0.6942
15, 21, sp1-5 ppi1, 0.7096667
16, 21, Wt, 0.7246667
17, 56, ppi1, 0.6652
18, 56, sp1-1, 0.6848
19, 56, sp1-1 ppi1, 0.6816
20, 56, sp1-2 ppi1, 0.6926
21, 56, sp1-3 ppi1, 0.6945
22, 56, sp1-4 ppi1, 0.676
23, 56, sp1-5 ppi1, 0.6931667
24, 56, Wt, 0.6946667
25, 111, ppi1, 0.653
26, 111, sp1-1, 0.6704
27, 111, sp1-1 ppi1, 0.6704
28, 111, sp1-2 ppi1, 0.6756
29, 111, sp1-3 ppi1, 0.679
30, 111, sp1-4 ppi1, 0.664
31, 111, sp1-5 ppi1, 0.6805
32, 111, Wt, 0.677
33, 186, ppi1, 0.6132
34, 186, sp1-1, 0.633
35, 186, sp1-1 ppi1, 0.6298
36, 186, sp1-2 ppi1, 0.6402
37, 186, sp1-3 ppi1, 0.6435
38, 186, sp1-4 ppi1, 0.6278
39, 186, sp1-5 ppi1, 0.6478333
40, 186, Wt, 0.6403333
41, 281, ppi1, 0.5636
42, 281, sp1-1, 0.587
43, 281, sp1-1 ppi1, 0.5828
44, 281, sp1-2 ppi1, 0.5906
45, 281, sp1-3 ppi1, 0.5968333
46, 281, sp1-4 ppi1, 0.5838
47, 281, sp1-5 ppi1, 0.5983333
48, 281, Wt, 0.5948333")

for_plot %>%
 ggplot()+
  geom_line(aes(x = Time, y = Mean, col = Mutant)) +
  geom_point(aes(x = Time, y = Mean, col = Mutant)) + 
  labs(title = "Effective PSII Quantum Yield across SP1 Mutants", 
       y = "Effective PSII Quantum Yield",
       x = "Actinic PPFD") +
  scale_color_hue(
    breaks = c("ppi1", "sp1-1", "sp1-1 ppi1", "sp1-2 ppi1",
               "sp1-3 ppi1", "sp1-4 ppi1", "sp1-5 ppi1", "Wt"),
    labels = c("ppi1", "*sp1-1*", "*sp1-1 ppi1*", "*sp1-2 ppi1*",
               "*sp1-3 ppi1*", "*sp1-4 ppi1*", "*sp1-5 ppi1*", "*Wt*")
  ) +
  theme(plot.title = element_text(hjust = 0.5)) +
  theme(legend.text = element_markdown())

This works also for parts of the text, e.g., if you wanted SP1 to be in italics in the title, you could do it like so.


for_plot %>%
  ggplot()+
  geom_line(aes(x = Time, y = Mean, col = Mutant)) +
  geom_point(aes(x = Time, y = Mean, col = Mutant)) + 
  labs(title = "Effective PSII Quantum Yield across *SP1* Mutants", 
       y = "Effective PSII Quantum Yield",
       x = "Actinic PPFD") +
  scale_color_hue(
    breaks = c("ppi1", "sp1-1", "sp1-1 ppi1", "sp1-2 ppi1",
               "sp1-3 ppi1", "sp1-4 ppi1", "sp1-5 ppi1", "Wt"),
    labels = c("ppi1", "*sp1-1*", "*sp1-1 ppi1*", "*sp1-2 ppi1*",
               "*sp1-3 ppi1*", "*sp1-4 ppi1*", "*sp1-5 ppi1*", "*Wt*")
  ) +
  theme(plot.title = element_markdown(hjust = 0.5)) +
  theme(legend.text = element_markdown())

回答2:

You may want to try genuine R plots, whose functions IMO might be less confusing and easier to learn, and which are definitely far better to customize.

There are two steps, defining labels and colors, then the plot with the legend.

# define labels and colors beforehand
mutants <- sort(unique(edtct3$Mutant))  # unique and alph. sorted mutants
clr <- hcl.colors(8, "Spectral")

op <- par(mar=c(5, 5, 4, 7.5))  # modify margins of plot region (B, L, T, R)
# plot
with(edtct3, plot(x=Time, y=Mean, type="n",  ## empty plot: type="n" 
                  main="Effective PSII Quantum Yield across SP1 Mutants",
                  ylab="Effective PSII Quantum Yield",
                  xlab="Actinic PPFD"))
# lines and points: loop over the mutants with an `sapply`
# the actual function is `lines()`
sapply(seq(mutants), function(x)  ## `seq(mutants)` makes a loop sequence over the mutants
  with(edtct3[edtct3$Mutant == mutants[x], ],  ## subsetting
       lines(x=Time, y=Mean, type="o", pch=16, col=clr[x])))  ## type="o" makes lines and points
# legend
legend(x=20.5, y=1.69, xpd=TRUE, legend=labs, pch=15, col=clr, cex=.9, 
       text.font=c(1, rep(3, 7)))  ## recall the "face" vector from former question
par(op)  # reset margins of plot region

Yields

Data:

edtc3 <- structure(list(Time = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 
6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 
6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 
11, 11, 11, 11, 11, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 
19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 
19, 19, 19, 19, 19, 19, 19), Mutant = c("sp2-3 ppi1", "ppi1", 
"WT", "sp2-6 ppi1", "sp2-4", "WT", "sp2-3 ppi1", "sp2-8 ppi1", 
"sp2 ppi1", "ppi1", "sp2-6 ppi1", "sp2-8 ppi1", "sp2 ppi1", "sp2-6 ppi1", 
"sp2-5 ppi1", "WT", "sp2-4", "sp2 ppi1", "sp2-4", "sp2-5 ppi1", 
"sp2-5 ppi1", "sp2-4", "sp2 ppi1", "WT", "sp2-6 ppi1", "sp2-8 ppi1", 
"sp2-3 ppi1", "sp2-8 ppi1", "ppi1", "ppi1", "sp2-3 ppi1", "sp2-5 ppi1", 
"sp2-5 ppi1", "sp2-6 ppi1", "ppi1", "WT", "sp2-8 ppi1", "sp2-8 ppi1", 
"sp2-3 ppi1", "sp2 ppi1", "ppi1", "sp2-6 ppi1", "WT", "sp2-8 ppi1", 
"WT", "sp2-3 ppi1", "sp2-5 ppi1", "ppi1", "sp2-3 ppi1", "sp2-6 ppi1", 
"sp2-5 ppi1", "sp2-3 ppi1", "sp2 ppi1", "sp2-5 ppi1", "sp2 ppi1", 
"ppi1", "sp2-4", "sp2-4", "sp2-4", "sp2-4", "WT", "sp2 ppi1", 
"sp2-6 ppi1", "sp2-8 ppi1", "sp2 ppi1", "sp2-4", "sp2-4", "sp2-8 ppi1", 
"sp2-4", "sp2-3 ppi1", "sp2-8 ppi1", "sp2-4", "WT", "sp2 ppi1", 
"ppi1", "sp2 ppi1", "sp2-5 ppi1", "WT", "sp2-3 ppi1", "sp2-3 ppi1", 
"sp2-3 ppi1", "sp2-6 ppi1", "sp2-5 ppi1", "ppi1", "ppi1", "sp2-8 ppi1", 
"sp2 ppi1", "WT", "WT", "sp2-6 ppi1", "sp2-5 ppi1", "ppi1", "sp2-5 ppi1", 
"sp2-6 ppi1", "sp2-6 ppi1", "sp2-8 ppi1", "sp2-3 ppi1", "sp2 ppi1", 
"sp2-5 ppi1", "sp2-6 ppi1", "sp2-3 ppi1", "sp2-4", "sp2-4", "sp2-6 ppi1", 
"sp2-5 ppi1", "sp2-4", "sp2-8 ppi1", "ppi1", "ppi1", "WT", "sp2 ppi1", 
"sp2 ppi1", "ppi1", "sp2-6 ppi1", "ppi1", "sp2-4", "sp2-5 ppi1", 
"sp2-3 ppi1", "sp2-6 ppi1", "sp2-5 ppi1", "sp2-8 ppi1", "WT", 
"sp2 ppi1", "sp2-8 ppi1", "sp2-3 ppi1", "sp2-8 ppi1", "WT", "WT"
), Mean = c(0.91, 0.59, 1.14, 0.74, 1.08, 1.65, 0.77, 1.34, 0.65, 
0.61, 0.86, 1.3, 0.82, 0.84, 0.97, 1.29, 1.15, 0.84, 1, 1.04, 
0.78, 1.01, 1.02, 1.33, 0.88, 1.25, 0.78, 1.25, 0.8, 0.67, 0.85, 
0.9, 1.04, 0.84, 0.67, 1.65, 1.25, 1.34, 0.77, 1.02, 0.59, 0.88, 
1.33, 1.3, 1.29, 0.91, 0.78, 0.8, 0.78, 0.86, 0.9, 0.85, 0.84, 
0.97, 0.65, 0.61, 1.01, 1.08, 1.15, 1, 1.14, 0.82, 0.74, 1.25, 
1.02, 1.08, 1.15, 1.25, 1.01, 0.85, 1.25, 1, 1.29, 0.84, 0.59, 
0.82, 1.04, 1.33, 0.77, 0.91, 0.78, 0.86, 0.78, 0.67, 0.61, 1.34, 
0.65, 1.65, 1.14, 0.84, 0.9, 0.8, 0.97, 0.74, 0.88, 1.3, 0.78, 
0.84, 1.04, 0.88, 0.91, 1.01, 1.15, 0.74, 0.78, 1, 1.3, 0.67, 
0.8, 1.14, 1.02, 0.82, 0.59, 0.84, 0.61, 1.08, 0.9, 0.77, 0.86, 
0.97, 1.34, 1.29, 0.65, 1.25, 0.85, 1.25, 1.65, 1.33)), row.names = c("17", 
"5", "1", "25", "10", "4", "18", "32", "15", "7", "27", "31", 
"14", "26", "24", "3", "9", "16", "11", "22", "21", "12", "13", 
"2", "28", "29", "19", "30", "6", "8", "20", "23", "221", "261", 
"81", "41", "291", "321", "181", "131", "51", "281", "210", "311", 
"33", "171", "211", "61", "191", "271", "231", "201", "161", 
"241", "151", "71", "121", "101", "91", "111", "110", "141", 
"251", "301", "132", "102", "92", "292", "122", "202", "302", 
"112", "34", "162", "52", "142", "222", "212", "182", "172", 
"192", "272", "213", "82", "72", "322", "152", "42", "113", "262", 
"232", "62", "242", "252", "282", "312", "193", "163", "223", 
"283", "173", "123", "93", "253", "214", "114", "313", "83", 
"63", "115", "133", "143", "53", "263", "73", "103", "233", "183", 
"273", "243", "323", "35", "153", "303", "203", "293", "43", 
"215"), class = "data.frame")

回答3:

Using a (very mildly) modified version of this function

Using this function, you can set the categories of interest as "plain" within the call to scale.

library(tidyverse)

toexpr <- function(x, plain = NULL) {
  getfun <- function(x) {
    ifelse(x == plain, "plain", "italic")
  }
  as.expression(unname(Map(function(f,v) substitute(f(v), list(f=as.name(f), v=as.character(v))), getfun(x), x)))
}

 ggplot(for_plot)+
  geom_line(aes(x = Time, y = Mean, col = Mutant)) +
  geom_point(aes(x = Time, y = Mean, col = Mutant)) + 
  scale_color_discrete(labels = toexpr(for_plot$Mutant, plain = 'Wt'))