I'm fairly new to R and I've been trying to make barplot with the code below:

Table

This table is what I'm trying to plot.

library(tidyverse)
library(parallel)
library(devtools)
library(scales)

peak_intersect_rep_elements <-
  tribble(
    ~Sample,                ~CellLine, ~Rep,  ~Total_peaks, ~Alu_intersect, ~L1_intersect, ~Antibody,
    "ADAR062", "HEK293xT", "rep1",   4407,           3329,        201, "p110/p150\nAb1",
    "ADAR062", "HEK293xT", "rep1",   19103,          3481,        8737, "p150\nAb3",
    "ADAR062", "HEK293xT", "rep1",   1782,           836,         109, "p110/p150\nAb4",
    "ADAR112", "HEK293xT", "rep1",   2269,           1852,        61, "p110/p150\nAb1",
    "ADAR112", "HEK293xT", "rep1",   28573,          5725,        17037, "p150\nAb3",
    "ADAR112", "HEK293xT", "rep1",   5115,           4448,        213, "p110/p150\nAb4",
    "ADAR112", "K562",     "rep1",   1367,           770,         49, "p110/p150\nAb1",
    "ADAR112", "K562",     "rep1",   12195,          2889,        5323, "p150\nAb3",
    "ADAR112", "K562",     "rep1",   1178,           656,         58, "p110/p150\nAb4",
    "ADAR004", "HEK293xT", "rep1",   4130,           3289,        136, "p110/p150\nAb1",
    "ADAR004", "HEK293xT", "rep2",   3447,           2816,        135, "p110/p150\nAb1",
    "ADAR004", "HEK293xT", "rep3",   4607,           3697,        176, "p110/p150\nAb1",
    "ADAR004", "HEK293xT", "rep1",   9711,           8450,        373, "p110/p150\nAb4",
    "ADAR004", "HEK293xT", "rep2",   7275,           6163,        294, "p110/p150\nAb4",
    "ADAR004", "HEK293xT", "rep3",   6789,           5704,        256, "p110/p150\nAb4"
  )  

Groupby

Here I'm averaging the values together and calculating the standard deviation for the table above.

total_peak_intersect_rep_elements_mean <- peak_intersect_rep_elements %>%
  group_by(Sample, CellLine, Antibody, Rep) %>%
  summarise(Mean_total_peaks = mean(Total_peaks), 
            Mean_alu_intersect = mean(Alu_intersect),
            Mean_l1_intersect = mean(L1_intersect),
            SD_total_peaks = sd(Total_peaks),
            SD_alu_intersect = sd(Alu_intersect),
            SD_l1_intersect = sd(L1_intersect)) %>%
  ungroup() %>%
  replace_na(list(SD_total_peaks = 0, SD_alu_intersect = 0, 
                  SD_l1_intersect = 0))

total_peak_intersect_rep_elements_mean

Plotting bargraph

Here I'm factoring the Rep column into levels and giving them names.

temp_plot <- total_peak_intersect_rep_elements_mean %>%
  mutate(Rep = factor(Rep, levels = c("rep1", "rep2", "rep3"),
                      labels = c("s1 (n = 1)", "s2 (n = 1)", 
                                 "s3 (n = 1)")))
  

I'm trying to fill by the Rep column here.

temp_plot %>%
  ggplot(aes(Antibody, Mean_total_peaks, fill=Rep)) +
  geom_bar(stat = "identity", position = "dodge", size = 0.3, color = "black") +
  geom_errorbar(aes(ymin=Mean_total_peaks - SD_total_peaks, 
                    ymax=Mean_total_peaks + SD_total_peaks), 
                width=0.6, size = 0.8,
                position=position_dodge(.9)) +
  facet_wrap(~CellLine, scales = 'free_x') +
  scale_fill_manual(values = c("s1 (n = 1)" = "#125863",
                               "s2 (n = 1)" = "#2BA8B3",
                               "s3 (n = 1)" = "#D5E9EB")) +
  scale_y_continuous(trans = "log10", labels=comma_format(accuracy = 1)) + 
  labs(y = "ADAR1 IP peaks", x = '', fill = "Replicate") +
  guides(color = F) +
  theme_minimal() +
  NULL

After this, I end up with a graph that looks like this.

However, as stated above, the error bars are not aligning properly. Could anyone help me out?