library(dygraphs)
## Warning: package 'dygraphs' was built under R version 4.2.3
library(readxl)
## Warning: package 'readxl' was built under R version 4.2.3
continuous = read_excel("SA_continuouspH_DV.xlsx")
continuous
## # A tibble: 40 × 4
##      Day Gouda Queso_fresco Kombucha
##    <dbl> <dbl>        <dbl>    <dbl>
##  1     0  5.07         4.04     3.67
##  2     3  4.21         3.87     2.91
##  3     7  4.02         4.02     2.52
##  4    10  3.98         4.07     2.57
##  5    14  4.09         4.13     2.57
##  6    14  5.17         4.3      3.49
##  7    17  4.88         4.24     3.28
##  8    21  4.51         4.13     3.05
##  9    24  4.41         4.05     3.02
## 10    28  4.37         4.03     2.95
## # ℹ 30 more rows

#Original draft of graph

dygraph(continuous, main = "Acidifcation of kombucha cultures in different substrates", ylab = "pH", xlab = "Day")  %>%
dyLegend(show = "follow", hideOnMouseOut = TRUE)

#Final version of graph with feedback taken into consideration

dygraph(continuous, main = "Comparing acidification of kombucha cultures in whey substrate compared to the model system, kombucha", ylab = "pH", xlab = "Day")  %>%
dyLegend(show = "always", hideOnMouseOut = TRUE, width = 120) %>%
dyGroup(c("Gouda", "Queso_fresco", "Kombucha"), drawPoints = TRUE, color = c("green", "purple", "blue")) %>%
dyHighlight(highlightSeriesOpts = list(strokeWidth = 3))

Caption: This interactive plot is displaying the acidification of kombucha cultures being introduced to a new substrate, whey, a by-product of cheesemaking, during a 112 day experiment. A total of eight batches (batch = 14 days) or culture repitchings were performed, with a new batch indicated by the line that connects the end point of one batch and starting point of another. Kombucha was fermented alongside the new substrates for three batches to act as a model system and point of comparison for the microbes fermentation performance. We can see the starting pH of the kombucha compared to the two whey types is largely different, although each whey type follows a similar acidification trend as the model, where it starts at a higher pH than it ends. We can also see over time the culture is able to acidify more in the new substrates, although the pattern of acidification we see in the gouda whey is more what we would expect to see as a culture adapts to a new environment and becomes able to create more metabolites. A significant point to mention is the last two batches of gouda acidified below pH 4, which is a safety marker that commercial food and beverage producers try and reach to ensure the safety of a product. This provides evidence the fermented whey product could be safe against the growth of foodborne pathogens.