How to draw facet_wrap with labels like facet_grid (independent y-axis)

I have data on gene expression levels (TPM value), which matrix consists of 2 cell lines and type. (experiment VS control)

![](https://i.stack.imgur.com/z7ePe.png)

My toy matrix

I'd like to compare the TPM value between KD and the experiment(KD) for each gene type.Additionally, because the two cell lines share the same gene type, I also want to draw them parallel.To draw them with a free-y-axis, I should use facet_wrap instead of facet_gridbut for facet_wrap, I found that I cannot make the same y labels as facet_grid can.

t1 <- ggplot(TPM_matrix, aes(x=Type, y=log10(TPM_value)),group=Type)+
  geom_point(aes(color=Type)) + 
  ggtitle("TPM levels") + 
  facet_wrap(Cell_Line ~ gene_name, ncol=4, scales="free_y") +
  theme(strip.background = element_blank(), 
        strip.text.y = element_text(size=12,face='bold'),
        axis.text.x=element_blank(), legend.position = 'right',
        legend.title=element_text(size=13),legend.text=element_text(size=13),
        plot.title = element_text(color = "black",hjust = 0.5, vjust=1, size = 20, face = 'bold'))

the result of t1

I can see each figure has its own cell line and gene name items.. but It is duplicated so I want to make them to share the x and y axis like t2

t2 <- ggplot(TPM_matrix, aes(x=Type, y=log10(TPM_value)),group=Type)+
  geom_point(aes(color=Type)) + 
  ggtitle("TPM levels") + 
  facet_grid(Cell_Line ~ gene_name, scales="free_y") +
  theme(strip.background = element_blank(), 
        strip.text.y = element_text(size=12,face='bold'),
        axis.text.x=element_blank(), legend.position = 'right',
        legend.title=element_text(size=13),legend.text=element_text(size=13),
        plot.title = element_text(color = "black",hjust = 0.5, vjust=1, size = 20, face = 'bold'))

the result of t2

but the result of t2 (facet_grid) doesn't offer a free-y axis,

I want to make t1 figure with t2 labels..

What I want to draw

What should I do? I need some help

One option is ggh4x::facet_grid2 which adds the option to have "independent" scales to facet_grid:

library(ggh4x)
#> Loading required package: ggplot2
library(ggplot2)

set.seed(123)

TPM_matrix <- data.frame(
  Type = rep(c("KD", "WT"), each = 4),
  Cell_Line = rep(c("BT20", "HEK292"), each = 8),
  gene_name = c("BRCA2", "CDC42", "THBS1", "TP53"),
  TPM_value = 10^(runif(16, 1, 4))
)

ggplot(TPM_matrix, aes(x = Type, y = log10(TPM_value)), group = Type) +
  geom_point(aes(color = Type)) +
  ggtitle("TPM levels") +
  facet_grid2(Cell_Line ~ gene_name, scales = "free_y", independent = "y") +
  theme(
    strip.background = element_blank(),
    strip.text.y = element_text(size = 12, face = "bold"),
    axis.text.x = element_blank(), legend.position = "right",
    legend.title = element_text(size = 13), legend.text = element_text(size = 13),
    plot.title = element_text(color = "black", hjust = 0.5, vjust = 1, size = 20, face = "bold")
  )

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