How to perform Post Hoc test, Tukey in agricolae package?

Question

[WUSCHEL]

How to perform a post-hoc test after TW ANOVA in R.

    structure(list(Treatment = structure(c(3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L), .Label = c("Control", "Nitrogen", "Salt"
), class = "factor"), Stage = structure(c(1L, 1L, 1L, 2L, 2L, 
2L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 2L, 2L, 3L, 3L, 3L, 1L, 1L, 1L, 
2L, 2L, 2L, 3L, 3L, 3L), .Label = c("Green", "Pink", "Red"), class = "factor"), 
    Chlorophyll = c(0.2, 0.3, 0.4, 0.5, 0.3, 0.2, 0.5, 0.6, 0.7, 
    0.4, 0.6, 0.9, 0.2, 0.3, 0.5, 0.4, 0.2, 0.3, 0.5, 0.6, 0.8, 
    0.5, 0.4, 0.6, 0.2, 0.3, 0.1)), .Names = c("Treatment", "Stage", 
"Chlorophyll"), class = "data.frame", row.names = c(NA, -27L))

I want to export ANOVA table and especially mean comparison results to a csv, and

Also, can we plot the graphs for each stage with the group numbers (mean separation groups) like this

[Jean-Karim Heriche]

Those are not really bioinformatics questions and may be more suitable for an R programming forum. I am not entirely sure what you're after but it seems to me that you're looking for Tukey Honest Significant Differences available in the functions TukeyHSD() in base R or HSD.test() in package agricolae. Here are two tutorials that you may find useful:
Two-way ANOVA test in R
Post-Hoc Analysis with Tukey’s Test