How to use names and rownames of a dataframe for the aes of ggplot?

Question

I have a dataframe enrichment_df that looks like this

                                         meclocycline pimozide isocorydine alvespimycin
day1_d         


        

Answer 1

Whenever using ggplot you should have your data in long format:

enrichment_df[ "day" ] <- rownames(enrichment_df)
df.molten <- melt( enrichment_df, id.vars="day", value.name="Enrichment", variable.name="Antibiotics" )

head(df.molten)
                                       day  Antibiotics Enrichment
1       day1_day3__sham3_strict_enrichment meclocycline     -0.869
2 hour4_day1_day3__sham3_strict_enrichment meclocycline     -0.294
3      day7_day14__sham3_strict_enrichment meclocycline     -0.333

This can be plotted by

ggplot(df.molten, aes( x = Antibiotics, y = Enrichment, fill = day ) ) + 
  geom_bar( position = "identity", stat = "identity", alpha = .3 )

I'm not sure though if position = "identity" with negative values is what you are looking for.