I am trying to put Several RColorBrewer Palettes that goes from lower tones to darker tones in one ggplot. But so far I've been unsuccessful and I've found that I can only use one.
My data set data:
data <- wrapr::build_frame(
"ID" , "Treatment", "conc" , "relabs" |
1 , "A" , "NK" , 0.9552 |
2 , "A" , "NK" , 1.016 |
3 , "A" , "NK" , 1.069 |
4 , "A" , "NK" , 1.029 |
5 , "A" , "NK" , 0.9992 |
6 , "A" , "NK" , 1.036 |
7 , "A" , "NK" , 0.9867 |
8 , "A" , "NK" , 0.9082 |
9 , "A" , "100 µM" , 0.9549 |
10 , "A" , "100 µM" , 0.9016 |
11 , "A" , "100 µM" , 0.9058 |
12 , "A" , "100 µM" , 0.9029 |
13 , "A" , "100 µM" , 0.8595 |
14 , "A" , "100 µM" , 0.8643 |
15 , "A" , "100 µM" , 0.8687 |
16 , "A" , "100 µM" , 0.9319 |
17 , "A" , "10 µM" , 0.8128 |
18 , "A" , "10 µM" , 0.805 |
19 , "A" , "10 µM" , 0.7765 |
20 , "A" , "10 µM" , 0.8065 |
21 , "A" , "10 µM" , 0.8153 |
22 , "A" , "10 µM" , 0.8045 |
23 , "A" , "10 µM" , 0.7827 |
24 , "A" , "10 µM" , 0.8017 |
25 , "A" , "10 µM X" , 0.00229 |
26 , "A" , "10 µM X" , 0.0002057 |
27 , "A" , "10 µM X" , -0.01033 |
28 , "A" , "10 µM X" , -0.003444 |
29 , "A" , "10 µM X" , -0.01401 |
30 , "A" , "10 µM X" , -0.007581 |
31 , "A" , "10 µM X" , -0.01063 |
32 , "A" , "10 µM X" , -0.01012 |
33 , "A" , "100 µM Y", 0.005991 |
34 , "A" , "100 µM Y", 0.01108 |
35 , "A" , "100 µM Y", 0.003925 |
36 , "A" , "100 µM Y", 0.02162 |
37 , "A" , "100 µM Y", 0.02916 |
38 , "A" , "100 µM Y", 0.01679 |
39 , "A" , "100 µM Y", 0.03044 |
40 , "A" , "100 µM Y", 0.01541 |
41 , "B" , "NK" , 1.038 |
42 , "B" , "NK" , 0.9651 |
43 , "B" , "NK" , 0.9948 |
44 , "B" , "NK" , 0.9688 |
45 , "B" , "NK" , 0.9727 |
46 , "B" , "NK" , 0.9985 |
47 , "B" , "NK" , 1.035 |
48 , "B" , "NK" , 1.027 |
49 , "B" , "100 µM" , 0.3466 |
50 , "B" , "100 µM" , 0.3429 |
51 , "B" , "100 µM" , 0.3131 |
52 , "B" , "100 µM" , 0.3302 |
53 , "B" , "100 µM" , 0.3204 |
54 , "B" , "100 µM" , 0.3265 |
55 , "B" , "100 µM" , 0.3238 |
56 , "B" , "100 µM" , 0.3425 |
57 , "B" , "10 µM" , 0.7703 |
58 , "B" , "10 µM" , 0.7484 |
59 , "B" , "10 µM" , 0.76 |
60 , "B" , "10 µM" , 0.7915 |
61 , "B" , "10 µM" , 0.7664 |
62 , "B" , "10 µM" , 0.7407 |
63 , "B" , "10 µM" , 0.7726 |
64 , "B" , "10 µM" , 0.8036 |
65 , "B" , "10 µM X" , -0.003965 |
66 , "B" , "10 µM X" , -0.001291 |
67 , "B" , "10 µM X" , 0.002101 |
68 , "B" , "10 µM X" , -0.001548 |
69 , "B" , "10 µM X" , 0.004782 |
70 , "B" , "10 µM X" , -0.006738 |
71 , "B" , "10 µM X" , -0.008429 |
72 , "B" , "10 µM X" , -0.009955 |
73 , "B" , "100 µM Y", 0.01063 |
74 , "B" , "100 µM Y", 0.008139 |
75 , "B" , "100 µM Y", 0.01149 |
76 , "B" , "100 µM Y", 0.01182 |
77 , "B" , "100 µM Y", 0.01418 |
78 , "B" , "100 µM Y", 0.009189 |
79 , "B" , "100 µM Y", 0.007849 |
80 , "B" , "100 µM Y", 0.0171 |
81 , "C" , "NK" , 0.9342 |
82 , "C" , "NK" , 1.033 |
83 , "C" , "NK" , 0.9425 |
84 , "C" , "NK" , 1 |
85 , "C" , "NK" , 1.082 |
86 , "C" , "NK" , 0.9697 |
87 , "C" , "NK" , 1.069 |
88 , "C" , "NK" , 0.9684 |
89 , "C" , "100 µM" , 1.31 |
90 , "C" , "100 µM" , 1.25 |
91 , "C" , "100 µM" , 1.305 |
92 , "C" , "100 µM" , 1.28 |
93 , "C" , "100 µM" , 1.293 |
94 , "C" , "100 µM" , 1.256 |
95 , "C" , "100 µM" , 1.35 |
96 , "C" , "100 µM" , 1.219 |
97 , "C" , "10 µM" , 0.9741 |
98 , "C" , "10 µM" , 1.066 |
99 , "C" , "10 µM" , 0.9849 |
100 , "C" , "10 µM" , 0.9737 |
101 , "C" , "10 µM" , 0.9619 |
102 , "C" , "10 µM" , 0.989 |
103 , "C" , "10 µM" , 0.9821 |
104 , "C" , "10 µM" , 1.026 |
105 , "C" , "10 µM X" , 0.137 |
106 , "C" , "10 µM X" , 0.1283 |
107 , "C" , "10 µM X" , 0.09757 |
108 , "C" , "10 µM X" , 0.1522 |
109 , "C" , "10 µM X" , 0.1411 |
110 , "C" , "10 µM X" , 0.1377 |
111 , "C" , "10 µM X" , 0.1222 |
112 , "C" , "10 µM X" , 0.1209 |
113 , "C" , "100 µM Y", -0.00434 |
114 , "C" , "100 µM Y", -0.009208 |
115 , "C" , "100 µM Y", 0.01106 |
116 , "C" , "100 µM Y", -0.0005099 |
117 , "C" , "100 µM Y", 0.001142 |
118 , "C" , "100 µM Y", -0.002433 |
119 , "C" , "100 µM Y", 0.009931 |
120 , "C" , "100 µM Y", -0.01025 |
121 , "D" , "NK" , 1.046 |
122 , "D" , "NK" , 1.032 |
123 , "D" , "NK" , 0.9685 |
124 , "D" , "NK" , 0.9981 |
125 , "D" , "NK" , 1.005 |
126 , "D" , "NK" , 1.001 |
127 , "D" , "NK" , 0.9329 |
128 , "D" , "NK" , 1.017 |
129 , "D" , "100 µM" , 0.1012 |
130 , "D" , "100 µM" , 0.1177 |
131 , "D" , "100 µM" , 0.09581 |
132 , "D" , "100 µM" , 0.09372 |
133 , "D" , "100 µM" , 0.1143 |
134 , "D" , "100 µM" , 0.1019 |
135 , "D" , "100 µM" , 0.08676 |
136 , "D" , "100 µM" , 0.09314 |
137 , "D" , "10 µM" , 0.461 |
138 , "D" , "10 µM" , 0.4717 |
139 , "D" , "10 µM" , 0.4536 |
140 , "D" , "10 µM" , 0.487 |
141 , "D" , "10 µM" , 0.5137 |
142 , "D" , "10 µM" , 0.4936 |
143 , "D" , "10 µM" , 0.4574 |
144 , "D" , "10 µM" , 0.4904 |
145 , "D" , "10 µM X" , -0.02192 |
146 , "D" , "10 µM X" , -0.02502 |
147 , "D" , "10 µM X" , -0.0238 |
148 , "D" , "10 µM X" , -0.01711 |
149 , "D" , "10 µM X" , -0.02345 |
150 , "D" , "10 µM X" , -0.01186 |
151 , "D" , "10 µM X" , -0.004447 |
152 , "D" , "10 µM X" , -0.01209 |
153 , "D" , "100 µM Y", -0.01495 |
154 , "D" , "100 µM Y", -0.01741 |
155 , "D" , "100 µM Y", -0.0101 |
156 , "D" , "100 µM Y", -0.007783 |
157 , "D" , "100 µM Y", 0.004533 |
158 , "D" , "100 µM Y", -0.01373 |
159 , "D" , "100 µM Y", -0.02207 |
160 , "D" , "100 µM Y", -0.01263 |
161 , "E" , "NK" , 1.03 |
162 , "E" , "NK" , 0.9683 |
163 , "E" , "NK" , 0.9915 |
164 , "E" , "NK" , 0.9887 |
165 , "E" , "NK" , 1.019 |
166 , "E" , "NK" , 1.007 |
167 , "E" , "NK" , 0.9909 |
168 , "E" , "NK" , 1.004 |
169 , "E" , "100 µM" , 0.7583 |
170 , "E" , "100 µM" , 0.8541 |
171 , "E" , "100 µM" , 0.822 |
172 , "E" , "100 µM" , 0.8506 |
173 , "E" , "100 µM" , 0.8122 |
174 , "E" , "100 µM" , 0.8442 |
175 , "E" , "100 µM" , 0.831 |
176 , "E" , "100 µM" , 0.8153 |
177 , "E" , "10 µM" , 0.9815 |
178 , "E" , "10 µM" , 0.9623 |
179 , "E" , "10 µM" , 0.97 |
180 , "E" , "10 µM" , 0.9798 |
181 , "E" , "10 µM" , 0.967 |
182 , "E" , "10 µM" , 0.9825 |
183 , "E" , "10 µM" , 1.01 |
184 , "E" , "10 µM" , 0.9284 |
185 , "E" , "10 µM X" , 0.2576 |
186 , "E" , "10 µM X" , 0.2454 |
187 , "E" , "10 µM X" , 0.2467 |
188 , "E" , "10 µM X" , 0.2544 |
189 , "E" , "100 µM Y", 0.005576 |
190 , "E" , "100 µM Y", 0.01025 |
191 , "E" , "100 µM Y", 0.00863 |
192 , "E" , "100 µM Y", 0.004152 )
data_summary <-
data %>%
group_by(Treatment, conc) %>%
dplyr::summarize(relabs_avg = mean(relabs),
relabs_sd = sd(relabs),
relabs_median = median(relabs),
relabs_mad = mad(relabs),
relabs_q1 = quantile(relabs, probs = c(0.25)),
relabs_q3 = quantile(relabs, probs = c(0.75)),
size = n()) %>%
dplyr::mutate(across(where(is.numeric), ~round(., digits = 3)))
data_summary
alpha <- 0.05
data_full <-
data %>%
group_by(Treatment, conc) %>%
dplyr:: summarize(mean = mean(relabs),
median = median(relabs),
lower = mean(relabs) - qt(1- alpha/2, (n() - 1))*sd(relabs)/sqrt(n()),
upper = mean(relabs) qt(1- alpha/2, (n() - 1))*sd(relabs)/sqrt(n()))
data_full
df<- merge(data_summary, data_full)
df
df_t_test <-
df_full %>%
group_by(Treatment, conc) %>%
do(tidy(t.test(.$relabs,
mu = 1 ,
alt = "less",
conf.level = 0.95, var.equal = FALSE)))
df_t_test
df_full<- merge(data, df)
df_full
df_full<- merge(data_full, df_t_test)
df_full
What I'm currently using:
df_full$Label <- NA
df_full$Label[df_full$mean <0]<-'ND'
df_full$Label[df_full$p.value<0.001 & is.na(df_full$Label)]<-'***'
df_full$Label[df_full$p.value<0.01 & is.na(df_full$Label)]<-'**'
df_full$Label[df_full$p.value<0.05 & is.na(df_full$Label)]<-'*'
breaks_y =c(0, 0.25, 0.5, 0.75, 1, 1.25, 1.5)
df_full$Label <- NA
df_full$Label[df_full$mean <0]<-'ND'
df_full$Label[df_full$p.value<0.001 & is.na(df_full$Label)]<-'***'
df_full$Label[df_full$p.value<0.01 & is.na(df_full$Label)]<-'**'
df_full$Label[df_full$p.value<0.05 & is.na(df_full$Label)]<-'*'
plot <-
ggplot(df_full, aes(x = factor (Treatment, level = c("A","B", "C", "D", "E")), y = mean, fill = conc))
geom_col(color = "black", position = position_dodge(0.8), width = 0.7)
geom_errorbar(aes(ymax = upper, ymin = lower), width = 0.27, position = position_dodge(0.8), color = "black", size = 0.7)
geom_text(aes(label = Label, group = conc),size = 3, position = position_dodge(width =0.8), color = "black", vjust =-2)
labs(x = "Treatment", y = "XXX", title = "YYY ", color = "ZZZ", fill = "ZZZ")
scale_y_continuous(limits = c(0, 1.5), breaks = breaks_y)
theme_bw()
theme(axis.text = element_text(size = 12, face = "bold"),
axis.title.y = element_text(size = 12, face ="bold"),
axis.title.x = element_text(size = 12, face ="bold"))
plot scale_fill_brewer(palette = "Blues")
Is there a way to put color palette "Blues" on A Treatment, "Greys" on B Treatment and so on? Or some kind of manual way to do that I wasn't able to find?
CodePudding user response：
You would really have to create your own combined Brewer palette and apply it to the interaction of the two grouping variables (conc and Treatment)
fills <- c(sapply(c("Blues", "Greys", "Purples", "Oranges", "Greens"),
function(x) brewer.pal(5, x)))
ggplot(df_full, aes(x = factor (Treatment, level = c("A","B", "C", "D", "E")),
y = mean, fill = interaction(conc, Treatment)))
geom_col(color = "black", position = position_dodge(0.8), width = 0.7)
geom_errorbar(aes(ymax = upper, ymin = lower), width = 0.27,
position = position_dodge(0.8), color = "black", size = 0.7)
geom_text(aes(label = Label, group = conc),size = 3,
position = position_dodge(width =0.8), color = "black", vjust =-2)
labs(x = "Treatment", y = "XXX", title = "YYY ", color = "ZZZ", fill = "ZZZ")
scale_y_continuous(limits = c(0, 1.5), breaks = breaks_y)
theme_bw()
theme(axis.text = element_text(size = 12, face = "bold"),
axis.title.y = element_text(size = 12, face ="bold"),
axis.title.x = element_text(size = 12, face ="bold"))
scale_fill_manual(values = fills)
Of course, the problem here is that your legend is now quite unwieldy. However, for a discrete color scale, it's difficult to get round this.
Possibly the cleanest way to achieve a similar effect is to fill according to treatment and use the alpha scale for conc
ggplot(df_full, aes(x = factor (Treatment, level = c("A","B", "C", "D", "E")),
y = mean, fill = Treatment, alpha = conc))
geom_col(color = "black", position = position_dodge(0.8), width = 0.7)
geom_errorbar(aes(ymax = upper, ymin = lower), width = 0.27,
position = position_dodge(0.8), color = "black", size = 0.7)
geom_text(aes(label = Label, group = conc),size = 3,
position = position_dodge(width =0.8), color = "black", vjust =-2)
labs(x = "Treatment", y = "XXX", title = "YYY ", color = "ZZZ", fill = "ZZZ")
scale_y_continuous(limits = c(0, 1.5), breaks = breaks_y)
theme_bw()
theme(axis.text = element_text(size = 12, face = "bold"),
axis.title.y = element_text(size = 12, face ="bold"),
axis.title.x = element_text(size = 12, face ="bold"))
scale_fill_brewer(palette ="Spectral" )
guides(fill = guide_none())
