CODEWITHSUNDEEP
rggplot2facet-gridgeom-hline
Cell
Cell

Reputation: 35

Draw hline with facet_grid

I'd like to draw hline with facet_wrap.

How can I add the 'reference value' of ref to each plot?

I want to add reference lines for 'RdRp', 'E', 'N', 'S'.

Both '4℃' and '22℃' use the same lines. For example, I want to draw a hline with yintercept=1.74E+05 for RdRp. And these lines in '4℃' and '22℃'are the same.

enter image description here

Here is my code without geom_hline.

library(reshape2)#melt,dcast
library(ggplot2)
library(ggh4x)#facet_nested

fig4ab=read.csv("fig4ab.csv")
ref=read.csv("ref.csv")
ref.melt=melt(ref, id.vars = c("Gene"))

#fig4ab
fig4ab.melt=na.omit(melt(fig4ab, id.vars = c("Sample", "Day", "Temp", "Vial")))
fig4ab.mean=dcast(fig4ab.melt, Day+Temp+Vial~variable, mean)
fig4ab.sd=dcast(fig4ab.melt, Day+Temp+Vial~variable, sd)
fig4ab.mean.melt=melt(fig4ab.mean, id.vars = c("Day", "Temp", "Vial"))
fig4ab.sd.melt=melt(fig4ab.sd, id.vars = c("Day", "Temp", "Vial"))

fig4ab.sd.melt[is.na(fig4ab.sd.melt)] = 0 

fig4ab.mean.total=dcast(fig4ab.mean.melt, Day+Temp~variable, mean)
fig4ab.sd.total=dcast(fig4ab.mean.melt, Day+Temp~variable, sd)
fig4ab.mean.total.melt=melt(fig4ab.mean.total, id.vars = c("Day", "Temp"))
fig4ab.sd.total.melt=melt(fig4ab.sd.total, id.vars = c("Day", "Temp"))

#STS 
ggplot(data = fig4ab.mean.total.melt, aes(x=Day, y=value))+
  geom_point()+
  geom_errorbar(aes(ymin = value - fig4ab.sd.total.melt$value, ymax = value + fig4ab.sd.total.melt$value), alpha=0.5, width=0.4)+
  facet_grid(variable~Temp)+
  labs(title = "Short-term stability")+
  xlab("Day") + ylab("copies/mL") +
  scale_x_continuous(breaks = c(0,1,2,5,7))+
  scale_y_continuous(limit = c(0,300000), breaks = c(0, 200000))+
  scale_colour_grey()+
  theme_bw()+
  theme(text=element_text(size= 11), legend.text=element_text(size=11), axis.text.x=element_text(size=11), axis.text.y=element_text(size=11), strip.text = element_text(
    size = 11))

dput of fig4ab

structure(list(Sample = 1:84, RdRp = c(192000, 188571.4, 180000, 
180000, 185142.9, 173142.9, 192000, 188571.4, 180000, 180000, 
185142.9, 173142.9, 166285.7, 176571.4, 161142.9, 197142.9, 198857.1, 
180000, 192000, 173142.9, 185142.9, 168000, 195428.6, 198857.1, 
190285.7, 183428.6, 195428.6, 186857.1, 178285.7, 178285.7, 164571.4, 
161142.9, 162857.1, 185142.9, 193714.3, 178285.7, 188571.4, 162857.1, 
169714.3, 190285.7, 173142.9, 181714.3, 226285.7, 209142.9, 216000, 
174857.1, 174857.1, 171428.6, 180000, 171428.6, 181714.3, 192000, 
181714.3, 181714.3, 181714.3, 181714.3, 178285.7, 117600, 125142.9, 
123085.7, 135428.6, NA, 144000, 125314.3, 135428.6, 128228.6, 
186857.1, 178285.7, 192000, 178285.7, 168000, 186857.1, 190285.7, 
181714.3, 173142.9, 149142.9, 145714.3, 144000, 169714.3, 159428.6, 
169714.3, 152571.4, 159428.6, 154285.7), E = c(159428.6, 168000, 
157714.3, 161142.9, 156000, 161142.9, 159428.6, 168000, 157714.3, 
161142.9, 156000, 161142.9, 154285.7, 157714.3, 148971.4, 186857.1, 
176571.4, 168000, 164571.4, 166285.7, 164571.4, 193714.3, 178285.7, 
185142.9, 178285.7, 161142.9, 168000, 171428.6, 168514.3, 176571.4, 
149828.6, 150857.1, 152571.4, 168000, 181714.3, 176571.4, 161142.9, 
161142.9, 156000, 162857.1, 171428.6, 168000, 195428.6, 188571.4, 
198857.1, 157714.3, 166285.7, 162857.1, 169714.3, 171428.6, 166285.7, 
178285.7, 180000, 178285.7, 166285.7, 162857.1, 162857.1, 111085.7, 
127885.7, 117257.1, 127714.3, 132000, 132000, 122400, 120857.1, 
122571.4, 176571.4, 168000, 161142.9, 152742.9, 159428.6, 161142.9, 
162857.1, 173142.9, 149314.3, 156000, 142285.7, 150514.3, 159428.6, 
160285.7, 168000, 152571.4, 156000, 140571.4), N = c(219428.6, 
214285.7, 195428.6, 214285.7, 214285.7, 205714.3, 219428.6, 214285.7, 
195428.6, 214285.7, 214285.7, 205714.3, 190285.7, 190285.7, 185142.9, 
207428.6, 212571.4, 207428.6, 202285.7, 200571.4, 197142.9, 243428.6, 
240000, 241714.3, 226285.7, 224571.4, 233142.9, 214285.7, 226285.7, 
216000, 190285.7, 192000, 198857.1, 210857.1, 202285.7, 224571.4, 
200571.4, 204000, 197142.9, 216000, 228000, 233142.9, 246857.1, 
264000, 258857.1, 221142.9, 210857.1, 222857.1, 226285.7, 222857.1, 
221142.9, 221142.9, 226285.7, 236571.4, 217714.3, 210857.1, 205714.3, 
142285.7, 135428.6, 133200, 168000, 166285.7, 164571.4, 145714.3, 
149314.3, 149142.9, 216000, 198857.1, 217714.3, 185142.9, 197142.9, 
200571.4, 212571.4, 221142.9, 209142.9, 183428.6, 173142.9, 176571.4, 
190285.7, 210857.1, 209142.9, 195428.6, 188571.4, 188571.4), 
    S = c(200571.4, 198857.1, 202285.7, 200571.4, 181714.3, 183428.6, 
    200571.4, 198857.1, 202285.7, 200571.4, 181714.3, 183428.6, 
    169714.3, 174857.1, 174857.1, 193714.3, 200571.4, 190285.7, 
    190285.7, NA, NA, 198857.1, 214285.7, 192000, 214285.7, 202285.7, 
    209142.9, 197142.9, 197142.9, 205714.3, 178285.7, 173142.9, 
    168000, 193714.3, 205714.3, 195428.6, 185142.9, 174857.1, 
    181714.3, 200571.4, 195428.6, 198857.1, 238285.7, 224571.4, 
    240000, 202285.7, 197142.9, 190285.7, 195428.6, 212571.4, 
    198857.1, 222857.1, 204000, 200571.4, 202285.7, 195428.6, 
    205714.3, 130285.7, 134742.9, 133371.4, 142285.7, NA, 152571.4, 
    140571.4, 138857.1, 138857.1, 195428.6, 188571.4, 192000, 
    195428.6, 185142.9, 186857.1, 205714.3, 200571.4, 200571.4, 
    164571.4, 166285.7, 156000, 195428.6, 186857.1, 183428.6, 
    176571.4, 168000, 162857.1), Day = c(0L, 0L, 0L, 0L, 0L, 
    0L, 0L, 0L, 0L, 0L, 0L, 0L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 5L, 5L, 
    5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
    5L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
    7L, 7L, 7L, 7L), Temp = c("4℃", "4℃", "4℃", "4℃", "4℃", 
    "4℃", "22℃", "22℃", "22℃", "22℃", "22℃", "22℃", "4℃", 
    "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", "22℃", 
    "22℃", "22℃", "22℃", "22℃", "22℃", "22℃", "22℃", "22℃", 
    "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", 
    "22℃", "22℃", "22℃", "22℃", "22℃", "22℃", "22℃", "22℃", 
    "22℃", "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", "4℃", 
    "4℃", "4℃", "22℃", "22℃", "22℃", "22℃", "22℃", "22℃", 
    "22℃", "22℃", "22℃", "4℃", "4℃", "4℃", "4℃", "4℃", 
    "4℃", "4℃", "4℃", "4℃", "22℃", "22℃", "22℃", "22℃", 
    "22℃", "22℃", "22℃", "22℃", "22℃"), Vial = c(1L, 1L, 
    1L, 2L, 2L, 2L, 3L, 3L, 3L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 6L, 
    6L, 7L, 7L, 7L, 8L, 8L, 8L, 9L, 9L, 9L, 10L, 10L, 10L, 11L, 
    11L, 11L, 12L, 12L, 12L, 13L, 13L, 13L, 14L, 14L, 14L, 15L, 
    15L, 15L, 16L, 16L, 16L, 17L, 17L, 17L, 18L, 18L, 18L, 19L, 
    19L, 19L, 20L, 20L, 20L, 21L, 21L, 21L, 22L, 22L, 22L, 23L, 
    23L, 23L, 24L, 24L, 24L, 25L, 25L, 25L, 26L, 26L, 26L, 27L, 
    27L, 27L, 28L, 28L, 28L)), class = "data.frame", row.names = c(NA, 
-84L))

dput of ref

structure(list(Gene = c("N", "S", "E", "RdRp"), reference.value = c(200913.5238, 
223204.6667, 154144.5238, 173597.1905), uncertainty = c(59085.3527, 
55078.11069, 43052.0553, 41084.84359)), class = "data.frame", row.names = c(NA, 
-4L))

Upvotes: 1

Views: 202

Answers (1)

stefan
stefan

Reputation: 125607

You could achieve your desired result by passing your ref dataframe to the data argument of geom_hline. To make this work with your data I had to do some data wrangling to convert your reference values to numerics and to rename the Gene variable to make the faceting work.

library(reshape2) # melt,dcast
library(ggplot2)
library(ggh4x) # facet_nested

ref$reference.value <- as.numeric(gsub("\\.E", "e", ref$reference.value))
ref$uncertainty <- as.numeric(gsub("\\.E", "e", ref$uncertainty))
names(ref)[1] <- "variable"
ref$variable <- trimws(ref$variable)
ref$variable <- factor(ref$variable, levels = levels(fig4ab.mean.total.melt$variable))

# STS
ggplot(data = fig4ab.mean.total.melt, aes(x = Day, y = value)) +
  geom_hline(data = ref, aes(yintercept = reference.value)) +
  geom_point() +
  geom_errorbar(aes(ymin = value - fig4ab.sd.total.melt$value, ymax = value + fig4ab.sd.total.melt$value), alpha = 0.5, width = 0.4) +
  facet_grid(variable ~ Temp) +
  labs(title = "Short-term stability") +
  xlab("Day") +
  ylab("copies/mL") +
  scale_x_continuous(breaks = c(0, 1, 2, 5, 7)) +
  scale_y_continuous(limit = c(0, 300000), breaks = c(0, 200000)) +
  scale_colour_grey() +
  theme_bw() +
  theme(text = element_text(size = 11), legend.text = element_text(size = 11), axis.text.x = element_text(size = 11), axis.text.y = element_text(size = 11), strip.text = element_text(
    size = 11
  ))

Upvotes: 2

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