根据剂量反应曲线绘制原始 x 轴（drc 包）

Question

我有一个数据集如下。我想使用

drc

包绘制剂量反应曲线以显示 IC50 值。

df <- structure(list(conc = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 
                                          1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 
                                          2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
                                          3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
                                          4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
                                          5L, 5L, 5L, 5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 
                                          6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
                                          7L, 7L, 7L, 7L, 7L, 7L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 11L, 
                                          11L, 11L, 11L, 11L, 11L, 11L, 11L, 8L, 8L, 8L, 8L, 8L, 8L, 8L, 
                                          8L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 
                                          10L, 10L, 10L), levels = c("0", "0.1", "1", "10", "100", "1000", 
                                                                     "10000", "30000", "60000", "90000", "100000", "DMSO"), class = "factor"), 
                       fl = c(100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 
                              100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 63.21225779, 
                              101.8706211, 126.2780865, 111.5314588, 96.09426602, 78.24238472, 
                              96.09755918, 100.5283698, 91.27381472, 97.37499067, 115.0726428, 
                              122.5959865, 85.41762336, 179.9769368, 98.35492747, 100.5908253, 
                              84.26773394, 101.4552505, 125.1702075, 95.88848656, 82.24099899, 
                              110.2141294, 79.66828574, 90.02040403, 94.98167177, 99.46936453, 
                              119.7006765, 130.5157993, 78.18920918, 96.01585941, 102.5847831, 
                              108.9026336, 101.5528383, 79.31066707, 115.2681603, 89.6393365, 
                              117.9085333, 96.37725618, 91.7460037, 102.0326665, 91.31663206, 
                              90.26150215, 97.92890336, 114.4366954, 96.87187883, 109.927939, 
                              107.3011341, 102.2116202, 96.90044379, 100.2864878, 92.65414961, 
                              96.18469623, 93.8303407, 140.0548471, 98.65695034, 92.83672632, 
                              106.3178975, 103.0082607, 99.91031153, 116.7370842, 100.0813435, 
                              101.2193641, 114.7206302, 100.5724823, 129.0270352, 101.4296353, 
                              78.85143217, 116.4561314, 110.9225058, 95.51300981, 95.82320759, 
                              112.0002344, 153.6020867, 88.55315754, 62.40109088, 77.81809955, 
                              82.93065795, 92.28863559, 68.89955766, 98.32670152, 100.4676841, 
                              51.65315094, 92.33042129, 115.9890869, 83.31973839, 53.25314434, 
                              168.4599862, 49.95222165, 76.48054079, 0.887138442, -0.584344871, 
                              0.416501996, 45.54363915, 23.61298376, 23.16807216, 4.571463311, 
                              3.184265707, 0.919448776, 0.451929132, -1.014153522, -1.039708501, 
                              1.397715644, 0.051578618, 0.790341673, 5.248865072, 46.02295576, 
                              44.89215709, 25.50864995, 51.47704304, 39.381729, 22.5317588, 
                              14.1313762, -0.42971322, 26.95053851, 36.55531489, 21.38622522, 
                              7.384904715, 1.105835897, 1.913830946, -0.168468303, -0.320132148, 
                              23.98090175, 8.798552887, 5.042674912, 2.967859167, -1.471078129, 
                              0.163655876, -0.326592551)), class = "data.frame", row.names = c(NA, 
                                                                                               -148L))

这个

df

数据框我想从中计算 IC50。我一直在使用以下代码：

library(drc)
model <- drm(fl ~ as.numeric(conc), data=df, fct=LL.4(names=c("Slope", "Lower Limit", "Upper Limit", "IC50")))

model
#note the IC50 value of 7.577

现在当我绘制模型时

plot(model, type="all", xlab="Concentration", ylab="Normalised Fluorescence", log="x")

这给出了对数 x 轴。当我试图通过将 log = "x" 更改为 log = "" 来回到我的原始轴时，我得到了这个：

但是回顾一下我最初的浓度，我的值是 0-90,000，而不是图表显示的 0-12。如何将 x 轴更改为我的实际浓度值？我的 IC50 是 7.577，这对于图中给出的比例来说是有意义的，但在我的实际浓度单位中却不是。那么我该如何将 IC50 值也转换回正确的比例呢？

Answer 1

要转换为

"numeric"

，您需要先转换

"factor"

s

as.character

，请参阅这些答案。

df$conc_num <- as.numeric(as.character(df$conc))

library(drc)
model <- drm(fl ~ conc_num, data=df, fct=LL.4(names=c("Slope", "Lower Limit", "Upper Limit", "IC50")))
plot(model, type="all", xlab="Concentration", ylab="Normalised Fluorescence", log='x')