Dose Reponse Curve
from datar.all import (
f,
tibble,
c,
NA,
head,
mutate,
log10,
pivot_longer,
is_na,
filter_,
rep,
seq,
paste0
)
from plotnine import *
from plotnine_prism import *
%run nb_helpers.py
set_option("figure_size", (6, 4))
df = (
tibble(
agonist=c(
1e-10, 1e-8, 3e-8, 1e-7, 3e-7, 1e-6, 3e-6, 1e-5, 3e-5, 1e-4, 3e-4
),
ctr1=c(0, 11, 125, 190, 258, 322, 354, 348, NA, 412, NA),
ctr2=c(3, 33, 141, 218, 289, 353, 359, 298, NA, 378, NA),
ctr3=c(2, 25, 160, 196, 345, 328, 369, 372, NA, 399, NA),
trt1=c(3, NA, 11, 52, 80, 171, 289, 272, 359, 352, 389),
trt2=c(5, NA, 25, 55, 77, 195, 230, 333, 306, 320, 338),
trt3=c(4, NA, 28, 61, 44, 246, 243, 310, 297, 365, NA),
)
>> mutate(log_agonist=log10(f.agonist))
>> pivot_longer(
[~f.agonist, ~f.log_agonist],
names_pattern=r"(.{3})([0-9])",
names_to=["treatment", "rep"],
values_to="response",
)
>> filter_(~is_na(f.response))
)
df >> head()
p = (
ggplot(df, aes(x="log_agonist", y="response")) +
geom_smooth(
aes(colour="treatment"),
se=False,
method=nls,
method_args=dict(minv=1.67, maxv=397, ec50=-7, hill_coeff=1)
)
)
p
# apply a manual colour scale to the curves
p = p + scale_colour_manual(
labels = c("No inhibitor", "Inhibitor"),
values = c("#00167B", "#9FA3FE")
)
p
# reset the colour scale, add the data points, then use a new colour scale
p = (
p
+ geom_point(aes(colour="treatment", shape="treatment"), size=3)
+ scale_colour_prism(
palette="winter_bright", labels=c("No inhibitor", "Inhibitor")
)
+ scale_shape_prism(labels=c("No inhibitor", "Inhibitor"))
)
p
# use the Winter Bright theme and make the size of all plot elements larger
p = p + theme_prism(palette = "winter_bright", base_size = 12)
p
# adjust the axis limits, major tick positions, and axis guide
p = p + scale_y_continuous(
limits = c(-100, 500),
breaks = seq(-100, 500, 100),
guide = guide_prism_offset()
)
p
# adjust the axis limits, major and minor tick positions, axis guide, and
# axis text (aka. label) appearance
p = p + scale_x_continuous(
limits=c(-10, -3),
breaks=seq(-10, -3),
guide=guide_prism_offset_minor(),
minor_breaks=log10(rep(seq(1, 9), 7) * (10. ** rep(seq(-10, -4), each=9))),
labels=paste0("e", seq(-10, -3))
)
p
# remove the y axis title and legend title, change the x axis title and
# move the legend to the top left
p = p + theme(
axis_title_y = element_blank(),
legend_title = element_blank(),
legend_position = (0.25, 0.8),
# legend_justification = c(0.05, 0.95)
) + labs(x = "[Agonist], M")
p
