How to plot two trend lines in a single graph in ggplot2?-CodePudding

I am plotting a line plot with a smooth trend line for gene expression data with two treatments and 3 samples. An example of the long format looks like this,

Group   Gene    Sample  exp
C   Gene_1  Sample1 0.8833248
C   Gene_2  Sample1 2.9193536
C   Gene_3  Sample1 -4.27416
S   Gene_1  Sample1 -1.6297201
S   Gene_2  Sample1 3.6535838
S   Gene_3  Sample1 -4.27416
C   Gene_1  Sample2 -0.3275709
C   Gene_2  Sample2 3.4885281
.
.
C   Gene_3  Sample3 -2.923909
S   Gene_1  Sample3 0.3514516
S   Gene_2  Sample3 2.981017
S   Gene_3  Sample3 -3.1599246

Here the issue is I can make a trend plot separately for each treatment but I have no clue how to plot the trend line of two treatments in the same graph. I did something like,

C_S<-ggplot(CS_long_fmt, aes(x=Sample, y=exp))  
geom_line(aes(group=Gene))  
stat_summary(aes(x=as.numeric(Sample)), fun=mean, geom='line',
           size=1, color='blue')

CodePudding user response：

To get separate trend lines for each Group (Treatment?) you have to add the group aesthetic to stat_summary.

Note: Additionally I mapped on the color aes to differentiate the lines.

library(ggplot2)

ggplot(CS_long_fmt, aes(x = Sample, y = exp))  
  geom_line(aes(group = Gene))  
  stat_summary(aes(x = Sample, group = Group, color = Group),
    fun = mean, geom = "line",
    size = 1
  )

DATA

CS_long_fmt <- structure(list(Group = c(
  "C", "C", "C", "S", "S", "S", "C", "C",
  "C", "S", "S", "S"
), Gene = c(
  "Gene_1", "Gene_2", "Gene_3", "Gene_1",
  "Gene_2", "Gene_3", "Gene_1", "Gene_2", "Gene_3", "Gene_1", "Gene_2",
  "Gene_3"
), Sample = c(
  "Sample1", "Sample1", "Sample1", "Sample1",
  "Sample1", "Sample1", "Sample2", "Sample2", "Sample3", "Sample3",
  "Sample3", "Sample3"
), exp = c(
  0.8833248, 2.9193536, -4.27416,
  -1.6297201, 3.6535838, -4.27416, -0.3275709, 3.4885281, -2.923909,
  0.3514516, 2.981017, -3.1599246
)), class = "data.frame", row.names = c(
  NA,
  -12L
))