I am trying to create a stacked barplot with ggplot in R. I have the following dataframe:
| Sample | Date | Organism | Antibiotic | Resistance |
|---|---|---|---|---|
| 1 | 01/01/2020 | E Coli | Amoxicillin | S |
| 1 | 01/01/2020 | E Coli | Gentamicin | S |
| 1 | 01/01/2020 | E Coli | Cefalexin | R |
| 2 | 01/01/2020 | S aureus | Amoxicillin | S |
| 2 | 01/01/2020 | S aureus | Gentamicin | S |
| 2 | 01/01/2020 | S aureus | Cefalexin | R |
| 3 | 01/01/2020 | E Coli | Amoxicillin | S |
| 3 | 01/01/2020 | E Coli | Gentamicin | S |
| 3 | 01/01/2020 | E Coli | Cefalexin | S |
| 4 | 02/01/2020 | S aureus | Amoxicillin | S |
| 4 | 02/01/2020 | S aureus | Gentamicin | S |
| 4 | 02/01/2020 | S aureus | Cefalexin | R |
| 5 | 02/01/2020 | E coli | Amoxicillin | R |
| 5 | 02/01/2020 | E coli | Gentamicin | S |
| 5 | 02/01/2020 | E coli | Cefalexin | R |
| 6 | 03/01/2020 | E coli | Amoxicillin | R |
| 6 | 03/01/2020 | E coli | Gentamicin | R |
| 6 | 03/01/2020 | E coli | Cefalexin | S |
| 7 | 04/01/2020 | E coli | Amoxicillin | S |
| 7 | 04/01/2020 | E coli | Gentamicin | S |
| 7 | 04/01/2020 | E coli | Cefalexin | S |
| 8 | 04/01/2020 | S aureus | Amoxicillin | S |
| 8 | 04/01/2020 | S aureus | Gentamicin | S |
| 8 | 04/01/2020 | S aureus | Cefalexin | S |
| 9 | 05/01/2020 | Kleb pneumo | Amoxicillin | S |
| 9 | 05/01/2020 | Kleb pneumo | Gentamicin | S |
| 9 | 05/01/2020 | Kleb pneumo | Cefalexin | S |
| 10 | 05/01/2020 | Kleb pneumo | Amoxicillin | R |
| 10 | 05/01/2020 | Kleb pneumo | Gentamicin | R |
| 10 | 05/01/2020 | Kleb pneumo | Cefalexin | R |
| 11 | 05/01/2020 | E coli | Amoxicillin | S |
| 11 | 05/01/2020 | E coli | Gentamicin | S |
| 11 | 05/01/2020 | E coli | Cefalexin | S |
| 12 | 06/01/2020 | S aureus | Amoxicillin | S |
| 12 | 06/01/2020 | S aureus | Gentamicin | S |
| 12 | 06/01/2020 | S aureus | Cefalexin | S |
| 13 | 06/01/2020 | Kleb pneumo | Amoxicillin | S |
| 13 | 06/01/2020 | Kleb pneumo | Gentamicin | S |
| 13 | 06/01/2020 | Kleb pneumo | Cefalexin | S |
| 14 | 06/01/2020 | Kleb pneumo | Amoxicillin | R |
| 14 | 06/01/2020 | Kleb pneumo | Gentamicin | R |
| 14 | 06/01/2020 | Kleb pneumo | Cefalexin | R |
I would like to create a stacked bar charts with ggplot by each Organism and each antibiotic with Date along the x-axis. I would like to do this for 1) by sample counts per day and 2) by percent of samples per day. Dates have already been converted to the date format using the as.Date function. I imagine it may be using a for loop including the following code, which currently just gives me a stacked percentage chart for Resistance and not by Organism and Antibiotic?
ggplot(sens_df, aes(fill=Resistance, , x=Date)) +
geom_bar(position="fill", stat="count") + scale_fill_brewer(palette = "Set3")
Thank you very much for your help!