# 解剖逻辑生长曲线

## 不辞山路远，踏雪也相过。

Posted by Chevy on December 5, 2022

# 我们先画几个图来说明一下

``````library(tidyverse)
theme_set(theme_minimal())

points <- tibble(
age = c(38, 45, 52, 61, 80, 74),
prop = c(0.146, 0.241, 0.571, 0.745, 0.843, 0.738))

colors <- list(
data = "#41414550",
# data = "grey80",
fit = "#414145")

ggplot(points) +
aes(x = age, y = prop) +
geom_point(size = 3.5, color = colors\$data) +
scale_x_continuous(
name = "Age in months",
limits = c(0, 96),
# Because age is in months, I want breaks to land on multiples
# of 12. The `Q` in `extended_breaks()` are "nice" numbers to use
# for axis breaks.
breaks = scales::extended_breaks(Q = c(24, 12))) +
scale_y_continuous(
name = "Intelligibility",
limits = c(0, NA),
labels = scales::percent_format(accuracy = 1))
``````

# 介绍一个计算DC50的包:`DRM`

`````` sar_data_drc <- sar_raw_file %>% mutate(Mean_value = rowMeans(dplyr::select(sar_raw_file, -c("Concentration (nM)", "DEG_ID")), na.rm = TRUE))

drc_model <- drm(Mean_value~ `Concentration (nM)`, DEG_ID, fct=LL.4(names=c("Slope", "Lower", "Upper", "ED50")), data = sar_data_drc)

results <- drc_model\$coefficients %>%
as.data.frame() %>%
rownames_to_column() %>% setNames(c("coefficients", "value")) %>%
mutate(coeff = str_split_fixed(coefficients, pattern = ":",n = 2)[,1]) %>%
mutate(DEG_ID = str_split_fixed(coefficients, pattern = ":",n = 2)[,2]) %>%
dplyr::select(c("value", "coeff", "DEG_ID")) %>%
reshape2::dcast(DEG_ID~coeff) %>%
rowwise() %>%
mutate(IC50 = ((Upper -Lower )/(0.5-Lower ) -1)^(1/Slope) *ED50) %>%
mutate(IC30 = ((Upper -Lower )/(0.7-Lower ) -1)^(1/Slope) *ED50) %>%
mutate(IC10 = ((Upper -Lower )/(0.9-Lower ) -1)^(1/Slope) *ED50) %>%
mutate(AUC = computeAUC(c(10000, 10000/3, 10000/(3^2), 10000/(3^3),
10000/(3^4), 10000/(3^5), 10000/(3^6),
10000/(3^7), 10000/(3^8), 10000/(3^9)),
area.type = "Fitted",
conc_as_log = F,
Hill_fit = c(-Slope, Upper, ED50))) %>%
cbind(data.frame(drc::ED(drc_model, 50)[,1], drc::ED(drc_model, 90)[,1]) %>% as.data.frame() %>% setNames(c("EC50", "EC90"))) %>%
dplyr::rename("Emax" = "Lower") %>%
mutate_at(c("Slope", "Emax", "Upper", "ED50", "IC50", "IC30", "IC10", "AUC","EC50", "EC90"), ~round(., digits = 3))
``````