Help with R code!!!
Hi all,
I am trying to make a histogram of some data I collected. I am trying to stratify my "baseline" data by biological replicate and all other data (a separate category called ExM) by gel. I want it to look something like what I've drawn below. This is the code I am currently working with and the current output. Any recommendations will be greatly appreciated!
# mean + SD per gel × tissue_type
gel_stats <- DAPI_Quant %>%
group_by(gel, tissue_type) %>%
summarise(
mean_avg = mean(ratio, na.rm = TRUE),
sd_avg = sd(ratio, na.rm = TRUE),
.groups = "drop"
)
# Convert gel to character
gel_stats$gel <- as.character(gel_stats$gel)
# Create color palette
unique_gels <- unique(gel_stats$gel)
# ExM palette (Dark2)
exm_palette <- scales::brewer_pal(type = "qual", palette = "Dark2")(length(unique_gels))
gel_colors <- setNames(exm_palette, unique_gels)
# Baseline override (curve color)
gel_colors["baseline"] <- "grey30"
# plot styling + axes
p <- ggplot() +
theme_classic(base_size = 10) +
theme(
legend.position = "right",
axis.title = element_text(size = 10),
axis.text = element_text(size = 10),
plot.margin = margin(10, 10, 10, 10)
) +
xlim(0.75,1.35) + ylim(0, 15)+
labs(
x = "XY Ratio",
y = "Density"
)
# histogram per gel
for (g in unique_gels) {
df_gel <- DAPI_Quant %>% filter(gel == g)
# Baseline bars grey, ExM bars keep their original color
hist_fill <- ifelse(g == "baseline", "grey30", gel_colors[g])
p <- p +
geom_histogram(
data = df_gel,
aes(x = ratio, y = after_stat(density)),
bins = 150,
fill = hist_fill,
alpha = 0.25,
color = NA
)
}
for (i in 1:nrow(gel_stats)) {
row <- gel_stats[i, ]
g <- row$gel
# Baseline curve grey, ExM curves keep their colors
curve_col <- ifelse(row$tissue_type == "baseline", "grey30", gel_colors[g])
p <- p + stat_function(
fun = dnorm,
args = list(mean = row$mean_avg, sd = row$sd_avg),
color = curve_col,
linewidth = ifelse(row$tissue_type == "baseline", 1.4, 1.1),
lineend = "round",
inherit.aes = FALSE
)
}
p
