This is the code for the calibration figure, and also shows code for plots comparing a two and three point calibration.
setwd("~/Box Sync/Ulmschneider manuscript/fig1_supp/threeptcalibration/")
set3 = read.csv("130803_nig_redo.csv")
set3$Type = as.character(set3$Type)
set3$Type[set3$Type == "daughter_F2" | set3$Type == "daughter_F3"] <- "follicle"
set3$Type[set3$Type == "daughter_F1"] <- "prefollicle"
This is the plot for the three point calibration.
library(ggplot2)
## Warning: package 'ggplot2' was built under R version 3.1.3
p3 = ggplot(set3, aes(x= pH, y = Ratio, fill = Type, colour = Type ))
p3 + geom_point(position = position_jitter(w = 0.01) ) + stat_smooth(method = "lm", se = FALSE) + theme_classic(base_size = 15 )
This is the plot for the two point calibration
set3.twopt = set3[set3$pH != 7.0,]
p4 = ggplot(set3.twopt, aes(x= pH, y = Ratio, fill = Type, colour = Type ))
p4 + geom_point(position = position_jitter(w = 0.01) ) + stat_smooth(method = "lm", se = FALSE) + theme_classic(base_size = 15 )
This code extracts the slope and y-intercept from the linear regression model
source("newpH.R")
## Warning: package 'plyr' was built under R version 3.1.3
lms = dlply(set3, .(Type), mylm)
coefs1= mycoefs(lms)
set3.twopt = set3[set3$pH != 7.0,]
lms2 = dlply(set3.twopt, .(Type), mylm)
coefs2 = mycoefs(lms2)
names(coefs1) <- c("cellType", "intercept", "slope", "rsquared")
#remames columns
names(coefs2) <- c("cellType", "intercept", "slope", "rsquared")
Three point calibration
coefs1
## cellType intercept slope rsquared
## 1 follicle -6.222341 1.0353002 0.9173353
## 2 prefollicle -5.741280 0.9542530 0.9032306
## 3 stem -5.784677 0.9537504 0.8522626
Two point calibration
coefs2
## cellType intercept slope rsquared
## 1 follicle -6.247494 1.0379101 0.9220061
## 2 prefollicle -5.776138 0.9578554 0.9091619
## 3 stem -5.684990 0.9446426 0.8673960
This code calculates the differences between the two and three point calibrations, and puts everything in a single data frame
diffSlope = coefs1$slope - coefs2$slope
diffInt = coefs1$intercept - coefs2$intercept
diffRsq = coefs1$rsquared - coefs2$rsquared
coefs1$calType = "threept"
coefs2$calType = "twopt"
allcoefs = rbind(coefs1, coefs2)
allcoefs$diffSlope = diffSlope
allcoefs$diffInt = diffInt
allcoefs$diffrsq = diffRsq
allcoefs
## cellType intercept slope rsquared calType diffSlope
## 1 follicle -6.222341 1.0353002 0.9173353 threept -0.002609893
## 2 prefollicle -5.741280 0.9542530 0.9032306 threept -0.003602363
## 3 stem -5.784677 0.9537504 0.8522626 threept 0.009107874
## 4 follicle -6.247494 1.0379101 0.9220061 twopt -0.002609893
## 5 prefollicle -5.776138 0.9578554 0.9091619 twopt -0.003602363
## 6 stem -5.684990 0.9446426 0.8673960 twopt 0.009107874
## diffInt diffrsq
## 1 0.02515352 -0.004670823
## 2 0.03485852 -0.005931296
## 3 -0.09968715 -0.015133362
## 4 0.02515352 -0.004670823
## 5 0.03485852 -0.005931296
## 6 -0.09968715 -0.015133362