growkar

growkar is an R-package to visualize and analyze growth curve data from timely recorded optical density by spectrophotometers.

Install

if(require("devtools")){
        devtools::install_github("sethiyap/growkar")
} else{
        install.packages("devtools")
        devtools::install_github("sethiyap/growkar")
}

Plot growth curve

Individual replicate

growkar::plot_growth_curve(dat_growth_curve = growkar::yeast_growth_data, palette_name="Set1")

With specific replicates

growkar::plot_growth_curve(dat_growth_curve = growkar::yeast_growth_data, average_replicates = FALSE, select_replicates = c("R1", "R2"), palette_name="Set1")

Average of replicates

# Vertical lines represent standard deviation

growkar::plot_growth_curve(dat_growth_curve = growkar::yeast_growth_data, average_replicates = TRUE, palette_name="Set1")

Computation of growth rate and generation time

Growth rates have often been used to evaluate the measure of fitness. Logarithmic phase of the curve is used to determine the growth-rate. Here, late lag-phase and early stationary-phase is defined as actively dividing log-phase (as shown in figure).

Log-phase start (T1): the time-point at which OD (OD1) is double to that of the OD at the initial time-point (i.e., 0 hour) Log-phase end (T2): the time-point at which the OD (OD2) becomes twice of OD1.

Growth-rate is calculated as described in (Ng et al., 2016);

Growth rate (generation/hour); is the number of generations (doublings) per hour.

Doubling time (or generation time); is the time taken by the population to double:

The doubling time (minutes/doubling) is the reciprocal of the growth rate.

calculate_growth_rate

Individual replicate

cc <-  growkar::calculate_growth_rate(dat_growth_curve = growkar::yeast_growth_data)

knitr::kable(cc,"html", align = "l") %>%
    kableExtra::kable_styling(bootstrap_options = c("striped", "condensed", "responsive"), full_width = F,font_size =14,  stripe_color = "aquamarine3") %>%
    kableExtra::row_spec(0,bold = TRUE, italic = FALSE, color = "black") %>%
    kableExtra::column_spec(c(1, 5:6), bold=FALSE, color="blue")

condition1	replicate1	time1	time2	growth_rate	doubling_time
Cg	R1	4.0	5.5	0.531	33.995
Cg	R2	4.0	5.5	0.515	35.050
Cg	R3	4.5	5.5	0.556	32.503
CgFlu	R1	4.0	6.0	0.396	45.563
CgFlu	R2	4.0	5.5	0.399	45.266
CgFlu	R3	4.0	5.5	0.400	45.107
YPD	R1	0.0	0.0	NaN	NaN
YPD	R2	0.0	0.0	NaN	NaN
YPD	R3	0.0	0.0	NaN	NaN

With specific replicates

cc <- growkar::calculate_growth_rate(dat_growth_curve =     growkar::yeast_growth_data, average_replicates = FALSE, select_replicates = c("R1", "R2"))

knitr::kable(cc,"html", align = "l") %>%
    kableExtra::kable_styling(bootstrap_options = c("striped", "condensed", "responsive"), full_width = F,font_size =14,  stripe_color = "aquamarine3") %>%
    kableExtra::row_spec(0,bold = TRUE, italic = FALSE, color = "black") %>%
    kableExtra::column_spec(c(1,5:6), bold=FALSE, color="blue")

condition1	replicate1	time1	time2	growth_rate	doubling_time
Cg	R1	4	5.5	0.531	33.995
Cg	R2	4	5.5	0.515	35.050
CgFlu	R1	4	6.0	0.396	45.563
CgFlu	R2	4	5.5	0.399	45.266
YPD	R1	0	0.0	NaN	NaN
YPD	R2	0	0.0	NaN	NaN

Average of replicates

cc <- growkar::calculate_growth_rate(dat_growth_curve = growkar::yeast_growth_data, average_replicates = TRUE)

knitr::kable(cc,"html", align = "l") %>%
    kableExtra::kable_styling(bootstrap_options = c("striped", "condensed", "responsive"), full_width = F,font_size =14,  stripe_color = "aquamarine3") %>%
    kableExtra::row_spec(0,bold = TRUE, italic = FALSE, color = "black") %>%
    kableExtra::column_spec(c(1, 4:5), bold=FALSE, color="blue")

condition	time1	time2	growth_rate	doubling_time
Cg	4.5	5.5	0.560	32.248
CgFlu	4.0	5.5	0.397	45.501
YPD	0.0	0.0	NaN	NaN

calculate_growthrate_from_defined_time

Using user defined logphase start and end time-point growth rate and generation time can be computed.

Individual replicate

# Load logphase start-end from local file

logphase_dat <- system.file("extdata", "logphase_for_replicates.txt", package = "growkar")
logphase_tibble <- readr::read_delim(logphase_dat, delim="\t", col_names = TRUE)

cc <-  growkar::calculate_growthrate_from_defined_time(dat_growth_curve = growkar::yeast_growth_data,logphase_tibble, average_replicates = FALSE)

knitr::kable(cc,"html", align = "l") %>%
    kableExtra::kable_styling(bootstrap_options = c("striped", "condensed", "responsive"), full_width = F,font_size =14,  stripe_color = "aquamarine3") %>%
    kableExtra::row_spec(0,bold = TRUE, italic = FALSE, color = "black") %>%
    kableExtra::column_spec(c(1, 5:6), bold=FALSE, color="blue")

condition	replicate	Time1	Time2	growth_rate	doubling_time
Cg	R1	5.0	6.0	0.597	30
Cg	R2	5.0	6.0	0.577	31
Cg	R3	5.5	7.0	0.538	34
CgFlu	R1	6.0	7.0	0.370	49
CgFlu	R2	5.0	6.5	0.408	44
CgFlu	R3	5.5	6.5	0.397	45
YPD	R1	0.0	0.0	NaN	NaN
YPD	R2	0.0	0.0	NaN	NaN
YPD	R3	0.0	0.0	NaN	NaN

Average of replicates

# Load logphase start-end from local file

logphase_dat <- system.file("extdata", "logphase_for_replicates.txt", package = "growkar")
logphase_tibble <- readr::read_delim(logphase_dat, delim="\t", col_names = TRUE)

cc <-  growkar::calculate_growthrate_from_defined_time(dat_growth_curve = growkar::yeast_growth_data,logphase_tibble, average_replicates = TRUE)

knitr::kable(cc,"html", align = "l") %>%
    kableExtra::kable_styling(bootstrap_options = c("striped", "condensed", "responsive"), full_width = F,font_size =14,  stripe_color = "aquamarine3") %>%
    kableExtra::row_spec(0,bold = TRUE, italic = FALSE, color = "black") %>%
    kableExtra::column_spec(c(1, 4:5), bold=FALSE, color="blue")

condition	Time1	Time2	growth_rate	doubling_time
Cg	5.167	6.333	0.582	31
CgFlu	5.500	6.667	0.385	47
YPD	0.000	0.000	NaN	NaN