Reputation: 368
I am working with ggeffects package I have the following syntax
data_example <- structure(list(paciente = structure(c(6171, 6488, 6300, 6446,
6489, 6445, 6473, 6351, 6212, 6387), label = "Paciente", format.spss = "F6.0"),
edad_s1 = structure(c(69, 62, 60, 71, 67, 59, 63, 66, 67,
70), label = "Edad", format.spss = "F3.0"), sexo_s1 = structure(c(1L,
2L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 1L), .Label = c("Hombre",
"Mujer"), label = "Sexo", class = "factor"), grupo_int_v00 = structure(c(1L,
1L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L), .Label = c("A", "B"), label = "Grupo de intervención", class = "factor"),
time = c(0, 0, 0, 2, 2, 2, 1, 2, 1, 1), peso1 = c(89.9, 62,
91.5, 75.2, 68.2, 88.4, 93.6, 79, 88.3, 84.4), cintura1 = c(113,
90, 112, NA, 87.5, 116, 98.5, 104, 112.5, 108.5), tasis2_e = c(132,
132, 149, NA, 145, 137, 129, 152, 146, 129), tadias2_e = c(81,
58, 79, NA, 80, 60, 79, 87, 79, 68), p17_total = c(7, 9,
10, 10, 10, 10, 10, 7, 10, 11), geaf_tot = c(3412.59, 3524.48,
559.44, 5454.55, 4293.71, 839.16, 3146.85, 7552.45, 4335.66,
566.9), glucosa = c(102, 97, 89, NA, 88, 168, 104, NA, 114,
121), albumi = c(4.94, 4.68, 4.75, NA, 4.34, 5.06, 4.56,
NA, 5.06, 3.96), coltot = c(232, 253, 215, NA, 202, 287,
255, NA, 217, 147), hdl = c(59, 64, 68, NA, 71, 46, 61, NA,
40, 42), ldl_calc = c(143, 150, 127, NA, 114, NA, 170, NA,
143, 86), trigli = c(152, 195, 99, NA, 85, 378, 121, NA,
170, 93), hba1c = c(5.61, 5.66, 5.43, NA, 5.38, 8.14, 5.81,
NA, 6, 6.38), i_hucpeptide = c(988.91, 673.5, 1036.03, NA,
734.29, 1266.3, 610.9, NA, 1144.8, 672.08), i_hughrelin = c(1133.35,
1230.06, 1109.98, NA, 1064.79, 725.35, 1437.85, NA, 866.07,
822.83), i_hugip = c(2.67, 2.67, 2.67, NA, 2.67, 2.67, 2.67,
NA, 2.67, 2.67), i_huglp1 = c(145.43, 138.32, 194.14, NA,
99.37, 166.27, 218.33, NA, 184.04, 222.84), i_huglucagon = c(513.89,
357.35, 624.73, NA, 464.85, 448.49, 304.29, NA, 310.61, 426.52
), i_huinsulin = c(234.23, 229.06, 358.86, NA, 175.38, 466,
99.02, NA, 367.95, 77.33), i_huleptin = c(7898.28, 5211.27,
14670.25, NA, 7161.39, 3218.49, 2659.8, NA, 3766.01, 1207.58
), i_hupai1 = c(3468.4, 1977.9, 4101.1, NA, 1613.4, 2847.27,
2442.49, NA, 1953.26, 1752.88), i_huresistin = c(4783.28,
2676.05, 3064.57, NA, 2165.52, 3878.48, 8343.46, NA, 2822.68,
6496.73), i_huvisfatin = c(831.6, 649.45, 2270.65, NA, 1578.88,
9.63, 185.09, NA, 162.8, 8.64), col_rema = c(30, 39, 20,
NA, 17, NA, 24, NA, 34, 19), homa = c(1061.843, 987.503,
1419.491, NA, 685.931, 3479.467, 457.692, NA, 1864.28, 415.864
), i_pcr = c(0.05, NA, 0.27, NA, 0.03, 0.23, 0.04, NA, 0.09,
0.09), d_homa = c(NA, NA, NA, NA, -2.629, 33.042, -181.211,
NA, -929.683, -89.108), d_hughrelin = c(NA, NA, NA, NA, -213.59,
48.43, 95.27, NA, -228.62, -146.8), d_huinsulin = c(NA, NA,
NA, NA, 3.24, -68.79, -43.31, NA, -147.33, -7.46), d_hucpeptide = c(NA,
NA, NA, NA, 192.39, -263.54, -71.56, NA, -437.38, -215.44
), d_huglucagon = c(NA, NA, NA, NA, 38.99, -112.45, -10.75,
NA, -133.55, -259.73), d_huleptin = c(NA, NA, NA, NA, 409.76,
-1081.5, -1778.69, NA, -353.91, -679.7), d_huresistin = c(NA,
NA, NA, NA, 391.02, -155.41, -436.47, NA, -1137.79, -922.75
), d_huvisfatin = c(NA, NA, NA, NA, 457.54, -260.79, -341.02,
NA, -426.89, 0), d_glucosa = c(NA, NA, NA, NA, -2, 23, 3,
NA, -8, -13), d_coltot = c(NA, NA, NA, NA, -52, 36, -11,
NA, 15, -12), d_hdl = c(NA, NA, NA, NA, 1, 3, -1, NA, 1,
4), d_ldl_calc = c(NA, NA, NA, NA, -50, NA, -10, NA, 12,
-15), d_col_rema = c(NA, NA, NA, NA, -3, NA, 0, NA, 2, -1
), d_trigli = c(NA, NA, NA, NA, -14, 132, -1, NA, 8, -5),
d_hba1c = c(NA, NA, NA, NA, -0.11, -0.04, -0.18, NA, -1.76,
-0.67), d_tasis2_e = c(NA, NA, NA, NA, 0, 6, -1, 7, -21,
-9), d_tadias2_e = c(NA, NA, NA, NA, 0, 2, -8, 8, -10, -17
), d_peso1 = c(NA, NA, NA, -6, -2.3, 0.2, -11.4, 0.8, -4.1,
-9.3), d_cintura1 = c(NA, NA, NA, NA, -2.5, -4, -12.5, 6,
-3.5, -4.5), d_geaf_tot = c(NA, NA, NA, 699.31, 2055.95,
-2181.82, 1748.25, 3776.23, 867.13, -6593.94), d_p17_total = c(NA,
NA, NA, 1, 4, 5, 4, -5, 5, 2), d_hupai1 = c(NA, NA, NA, NA,
-185.03, 204.77, 202.01, NA, -1551.91, 57.2), d_hugip = c(NA,
NA, NA, NA, 0, 0, 0, NA, 0, 0), d_huglp1 = c(NA, NA, NA,
NA, -42.07, -163.02, 107.28, NA, -95.82, -87.5), d_pcr = c(NA,
NA, NA, NA, NA, NA, NA, NA, -0.18, -0.22), ln_trigli = c(5.024,
5.273, 4.595, NA, 4.443, 5.935, 4.796, NA, 5.136, 4.533),
ln_homa = c(6.968, 6.895, 7.258, NA, 6.531, 8.155, 6.126,
NA, 7.531, 6.03), ln_hba1c = c(1.725, 1.733, 1.692, NA, 1.683,
2.097, 1.76, NA, 1.792, 1.853), ln_geaf_tot = c(8.135, 8.167,
6.327, 8.604, 8.365, 6.732, 8.054, 8.93, 8.375, 6.34), i_ratiolg = c(6.969,
4.237, 13.217, NA, 6.726, 4.437, 1.85, NA, 4.348, 1.468)), row.names = c(NA,
-10L), class = c("tbl_df", "tbl", "data.frame"))
The mixed model I have created following the syntax
lme_peso <- lme(peso1 ~ sexo_s1 + edad_s1 + poly(time, 2)*grupo_int_v00 + p17_total,
random = ~ poly(time, 2)|paciente, control=lmeControl(opt="optim"),
data = dat_longer, subset = !is.na(peso1), na.action = na.omit)
And then to plot it
ggpredict(lme_peso, c("time [all]", "grupo_int_v00"), type="fixed") %>%
ggplot(aes(x = x, y = predicted, colour = group)) +
geom_point() +
geom_line() +
stat_smooth(method = "loess",se = T) +
labs(x = "time (months)", y = "Weight (kg)") +
scale_color_manual(labels = c("Control", "Intervention"), values = c("orange", "green")) +
geom_ribbon(aes(ymin = conf.low, ymax = conf.high, fill = F),alpha = 1/5) +
scale_x_continuous(breaks = 0:2, labels = c(0, 6, 12))
When I supress the arguments of fill in geom_ribbon the fill stays black. But I don't know how to manage to keep just one legend with 2 groups (Control and Intervention). I have the extra-added legend (with F in this case)
Thanks in advance
Upvotes: 1
Views: 507
Reputation: 3294
I couldn't run your code, but I rebuilt it with iris
.
Like Matt suggested, one thing would be, remove fill=F
:
ggplot(data=iris, aes(x = SepalLength , y = PetalLength, group=Name)) +
geom_point() +
geom_line() +
stat_smooth(method = "loess",se = T, aes(color=Name)) +
geom_ribbon(aes(ymin = 1, ymax = 3),alpha = 1/5) +
scale_x_continuous(breaks = 0:2, labels = c(0, 6, 12))
Or if you need it for some reason, use guides(fill="none")
:
ggplot(data=iris, aes(x = SepalLength , y = PetalLength, group=Name)) +
geom_point() +
geom_line() +
stat_smooth(method = "loess",se = T, aes(color=Name)) +
geom_ribbon(aes(ymin = 1, ymax = 3, fill=FALSE),alpha = 1/5) +
scale_x_continuous(breaks = 0:2, labels = c(0, 6, 12)) +
guides(fill="none")
Output:
Upvotes: 1