Customize Barplot in base function barplot() - r

Question

I have a date frame (df), with 2 columns: One numerical and one as.factor() with three levels:
Pre
Post
Blank
I want to make a barplot() with each factor colored to it's respective group (easy), and change the order of the plot so each factor appears next to each other (this is where I'm stuck).
I followed the same logic as I would with a boxplot(), but it does not appear to work the same. I also tried following examples from several stackoverflow threads, including (but not limited to) this one:
Re-ordering bars in R's barplot()
But still can't get it to work.
Here is what I've tried, and it works with the boxplot function quite well:
df <- read.table("https://pastebin.com/raw/zaETq28M", header = T)
df$Treatment <- as.factor(df$Treatment)
levels(df$Treatment) # note: I would like to display order to be: Pre, Post, then Blank.
df$Treatment <- ordered(df$Treatment, levels = c("Pre","Post","Blank")) # set to the right order
barplot(df$Cq,names.arg = df$Treatment ,col = df$Treatment, ylim=c(0,30), main = "Not the right order bar plot", cex.main=2)
In total, I should have 66 individual bars (which I do), but somehow, the order of the graph is not what I set, and the groups are still separated. How can I simply get 3 distinct groups? Meaning, first show all "Pre", then all "post", followed by "blank"
General questions for future posts:
How to get a get my graphs to be displayed on Stackoverflow when I post a question? For some reason, my posts never include my graphs.
Also, any kind suggestion on using color blind pallet would be great, but I can just do this manually if needed. Just curious if there is an automatic way of doing it, so I do not need to set it manually in all my graphs
Thank you for your help

Answer 1

Do you mean this?
First the Pre, then Post then blank. Within each group order is preserved. Legend added with blank == No Treatment.
df <- read.table("https://pastebin.com/raw/zaETq28M", header = T)
df_Pre <- df[which(df$Treatment == 'Pre'),]
df_Post <- df[which(df$Treatment == 'Post'),]
df_Blank <- df[which(df$Treatment == 'Blank'),]
ddf <- rbind(df_Pre, df_Post, df_Blank)
ddf$color <- c(rep('blue', nrow(df_Pre)), rep('red', nrow(df_Post)), rep('magenta', nrow(df_Blank)))
barplot(ddf$Cq, col = ddf$color, names = rownames(ddf))
legend("bottomleft",
legend = c("Pre-Treatmen", "Post-Treatment", 'No Treatment'),
fill = c("darkblue", "red","magenta"))