showing three factors in line graph - r

Question

I am trying to make a line graph with three factors. In addition, I would like to have my legend labels have two symbols.
This is the published example I am trying to emulate....
as you can see, each label has two symbols, one for each level of one factor. Furthermore, the same factor is shown twice on the same panel for each level, i.e. cultivar with two different levels of a factor.
I am trying to make one panel at a time, I will join them later and put the legend at the top like in the above example.
Here is the start of my attempt....
I have got my points on the graph, though im baffled as to how to make a line join through each cultivar, show error bars, and make the legend similar to the above example. I want the legend to have one label for each cultivar, but with two symbols, one symbol for Waterlogging and one for Non-waterlogging
structure(list(pot = c(41L, 42L, 43L, 44L, 61L, 62L, 63L, 64L,
45L, 46L, 47L, 48L, 65L, 66L, 67L, 68L, 49L, 50L, 51L, 52L, 69L,
70L, 71L, 72L, 53L, 54L, 55L, 56L, 73L, 74L, 75L, 76L, 57L, 58L,
59L, 60L, 77L, 78L, 79L, 80L, 81L, 82L, 83L, 84L, 101L, 102L,
103L, 104L, 85L, 86L, 87L, 88L, 105L, 106L, 107L, 108L, 89L,
90L, 91L, 92L, 109L, 110L, 111L, 112L, 93L, 94L, 95L, 96L, 113L,
114L, 115L, 116L, 97L, 98L, 99L, 100L, 117L, 118L, 119L, 120L
), rep = c(1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L, 2L, 3L, 4L, 1L,
2L, 3L, 4L), cultivar = structure(c(4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L,
4L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L,
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L), .Label = c("Dinninup", "Riverina",
"Seaton Park", "Yarloop"), class = "factor"), Waterlogging = structure(c(2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L,
2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L), .Label = c("Non-waterlogged",
"Waterlogged"), class = "factor"), P = c(12.1, 12.1, 12.1, 12.1,
12.1, 12.1, 12.1, 12.1, 15.17, 15.17, 15.17, 15.17, 15.17, 15.17,
15.17, 15.17, 18.24, 18.24, 18.24, 18.24, 18.24, 18.24, 18.24,
18.24, 24.39, 24.39, 24.39, 24.39, 24.39, 24.39, 24.39, 24.39,
48.35, 48.35, 48.35, 48.35, 48.35, 48.35, 48.35, 48.35, 12.1,
12.1, 12.1, 12.1, 12.1, 12.1, 12.1, 12.1, 15.17, 15.17, 15.17,
15.17, 15.17, 15.17, 15.17, 15.17, 18.24, 18.24, 18.24, 18.24,
18.24, 18.24, 18.24, 18.24, 24.39, 24.39, 24.39, 24.39, 24.39,
24.39, 24.39, 24.39, 48.35, 48.35, 48.35, 48.35, 48.35, 48.35,
48.35, 48.35), form = c(2.81, 2.64, 2.59, 3.28, 3.18, 2.57, 2.9,
3, 2.38, 2.72, 2.58, 2.73, 3.06, 3.01, 3.01, 2.77, 2.95, 2.36,
2.91, 2.38, 3.33, 3.19, 3.17, 3.16, 3.16, 3.2, 2.58, 3.71, 3.11,
2.7, 2.92, 1.93, 2.95, 2.57, 2.68, 2.48, 3.34, 2.75, 2.52, 1.88,
1.19, 0.57, 0.64, 0.66, 1.13, 1.28, 0.85, 0.96, 1.34, 2.14, 0.63,
1.27, 1.13, 0.64, 1.21, 1.95, 1.11, 0.91, 0.75, 0.63, 1.06, 1.07,
1.05, 0.8, 1.41, 1.13, 0.75, 0.89, 1.98, 1.27, 1.01, 1, 1.16,
0.64, 0.64, 1.02, 1.03, 1.13, 0.79, 0.6)), row.names = 41:120, class = "data.frame")
library(Rmisc)
library(ggplot2)
tglf3 <- summarySE(yar, measurevar="form", groupvars=c("P","cultivar","Waterlogging"),na.rm=TRUE)
ggplot(tglf3, aes(x=P, y=form)) +
geom_point(aes(colour = factor(Waterlogging),
shape=factor(cultivar)),size=3.5,position=position_dodge(1))+
geom_errorbar(aes(ymin=form-se, ymax=form+se),colour="black", width=.1,position=position_dodge(1))

Answer 1

Is this approaching what you're looking for?
library(tidyverse)
tglf3 <- summarySE(yar, measurevar="form", groupvars=c("P","cultivar","Waterlogging"),na.rm=TRUE)
Mostly, making use of dplyr::group_by can solve the point-line pairing:
tglf3 %>%
group_by(cultivar) %>%
ggplot(aes(x=P, y=form, colour=Waterlogging, shape=cultivar)) +
geom_errorbar(aes(ymin=form-se, ymax=form+se), colour="black", width=.6) +
geom_point(size=3.5) +
geom_line() +
theme_classic() +
theme(legend.position = 'top', legend.direction="vertical")
More formatting using scale_x_manual:
tglf3 %>%
unite(new, cultivar, Waterlogging, sep = ', ') %>%
group_by(new) %>%
ggplot(aes(x=P, y=form, colour=new, shape=new, linetype=new)) +
geom_errorbar(aes(ymin=form-se, ymax=form+se), colour="black", width=.6) +
geom_line(color="black") +
geom_point(size=3.5) +
scale_colour_manual(name = "Cultivar, Waterlogging",
labels = c("Riverina, Non-waterlogged", "Riverina, Waterlogged", "Yarloop, Non-waterlogged", "Yarloop, Waterlogged"),
values = c("blue", "red", "blue", "red")) +
scale_shape_manual(name = "Cultivar, Waterlogging",
labels = c("Riverina, Non-waterlogged", "Riverina, Waterlogged", "Yarloop, Non-waterlogged", "Yarloop, Waterlogged"),
values = c(19, 19, 17, 17)) +
scale_linetype_manual(name = "Cultivar, Waterlogging", values=c("longdash", "solid", "longdash", "solid")) +
theme_classic() +
theme(legend.position = 'top', legend.direction="vertical") +
guides(color=guide_legend(ncol=2))
Without %>%:
tglf4 <- unite(data = tglf3, new, cultivar, Waterlogging, sep = ', ')
tglf5 <- group_by(.data = tglf4, new)
ggplot(tglf5, aes(x=P, y=form, colour=new, shape=new, linetype=new)) +
geom_errorbar(aes(ymin=form-se, ymax=form+se), colour="black", width=.6) +
geom_line(color="black") +
geom_point(size=3.5) +
scale_colour_manual(name = "Cultivar, Waterlogging",
labels = c("Riverina, Non-waterlogged", "Riverina, Waterlogged", "Yarloop, Non-waterlogged", "Yarloop, Waterlogged"),
values = c("blue", "red", "blue", "red")) +
scale_shape_manual(name = "Cultivar, Waterlogging",
labels = c("Riverina, Non-waterlogged", "Riverina, Waterlogged", "Yarloop, Non-waterlogged", "Yarloop, Waterlogged"),
values = c(19, 19, 17, 17)) +
scale_linetype_manual(name = "Cultivar, Waterlogging", values=c("longdash", "solid", "longdash", "solid")) +
theme_classic() +
theme(legend.position = 'top', legend.direction="vertical") +
guides(color=guide_legend(ncol=2))
Using facet_grid (example using fake data):
tglf3 %>%
mutate(
form = form * 1.5
) %>%
bind_rows(tglf3, .id = 'species') %>% # Add fake data to the real data as an example
mutate(
species = case_when(species == 1 ~ 'O. sativus',
T ~ 'O. compressus')
) %>%
unite(new, cultivar, Waterlogging, sep = ', ') %>%
group_by(new) %>%
ggplot(aes(x=P, y=form, colour=new, shape=new, linetype=new)) +
geom_errorbar(aes(ymin=form-se, ymax=form+se), colour="black", width=.6) +
geom_line(color="black") +
geom_point(size=3.5) +
scale_colour_manual(name = "Cultivar, Waterlogging",
labels = c("Riverina, Non-waterlogged", "Riverina, Waterlogged", "Yarloop, Non-waterlogged", "Yarloop, Waterlogged"),
values = c("blue", "red", "blue", "red")) +
scale_shape_manual(name = "Cultivar, Waterlogging",
labels = c("Riverina, Non-waterlogged", "Riverina, Waterlogged", "Yarloop, Non-waterlogged", "Yarloop, Waterlogged"),
values = c(19, 19, 17, 17)) +
scale_linetype_manual(name = "Cultivar, Waterlogging", values=c("longdash", "solid", "longdash", "solid")) +
theme_classic() +
theme(legend.position = 'top', legend.direction="vertical") +
guides(color=guide_legend(ncol=2)) +
facet_grid(.~species)