Can you clarify what you mean by "remove this class from the output figure"? Do you mean removing the legend like in this example?
library(tidyverse)
df <- data.frame(
stringsAsFactors = FALSE,
set = c("12","13","123","124",
"1234","1235","12345","12346","123456","123457"),
val = c(49319, 98443, 18191, 8405, 2807, 2871, 425, 310, 50, 55),
log_val = c(4.69301426218799,
4.99318484013431,4.25985657385978,3.92453771777549,3.44824241263444,
3.45803319249651,2.62838893005031,2.49136169383427,
1.69897000433602,1.74036268949424),
class = as.factor(c("2-fold",
"2-fold","3-fold","3-fold","4-fold","4-fold",
"5-fold","5-fold","6-fold","6-fold"))
)
ggplot(df, aes(x = set, y = log_val, col = class)) +
geom_point(aes(colour = class), size = 4, show.legend = FALSE) +
labs(
x = "CP",
y = "CC") +
facet_grid(~ class , scales="free")

Created on 2021-03-09 by the reprex package (v1.0.0.9002)