Breakdown by genotype What follows is a generic description of what I did to calculate pH values from ratio values for each set of RNAi data.
setwd("~/Box Sync/Nystul_lab/R/pHdata")
source("calcpH.R")
source("calcpH2.R")
source("newpH.R")
## Warning: package 'plyr' was built under R version 3.1.3
source("doStats.R")
library(ggplot2)
## Warning: package 'ggplot2' was built under R version 3.1.3
This is an example of how to calculate pH values from a linear regression model for one of my Nhe2RNAi experiments. The rest of this file details the locations of the other two files and the same procedure would be used to generate the pHi values and then was combined into a final file called “160426_reanalysis_nhe2RNAi.csv”
new = read.csv("150504_pHraw.csv")
pnew <- splitp(new)
hnew <- splith(new)
plot the regression lines
ggplot(pnew, aes(x=nph, y = Ratio, fill = genotype )) + geom_point() + stat_smooth(method = "lm") + facet_wrap(~region)
Breakdown by genotype
pctrl <- pnew[pnew$genotype == "10930ctrl",]
poe <- pnew[pnew$genotype == "10930Nhe2RNAi",]
ctrl.lm <- all_lm(pctrl, pctrl$region)
mut.lm <- all_lm(poe, poe$region)
df.ctrl <- mycoefs(ctrl.lm)
df.ctrl$genotype <- "10930ctrl"
df.oe <- mycoefs(mut.lm)
df.oe$genotype <- "10930Nhe2RNAi"
df.all <- rbind(df.ctrl, df.oe)
names(df.all) = c("region", "int", "slope", "rsquared", "genotype")
merged = merge(hnew, df.all, by = c("region", "genotype"))
merged$calcpH = calclm(merged$Ratio, merged$slope, merged$int)
Did this three times for three different Ns
relevant .csv files are:
150504_pHraw.csv
150428_pHraw.csv
150505and0513_pHraw.csv
all combined are in… write.csv(rnaiAll, “160426_reanalysis_nhe2RNAi.csv”, row.names = FALSE)
This is the plot for the Nhe2RNAi pH data.
rnaiAll = read.csv("160426_reanalysis_nhe2RNAi.csv")
rnaiAll= read.csv("")
## Warning in file(file, "rt"): file("") only supports open = "w+" and open =
## "w+b": using the former
## Error in read.table(file = file, header = header, sep = sep, quote = quote, : no lines available in input
rnaiAll.clean = rnaiAll[rnaiAll$calcpH < 7.8 & rnaiAll$calcpH > 6.5,]
pvals = getpvals(rnaiAll.clean, myt)
summaryRNAi = ddply(rnaiAll.clean, .(genotype, region), summarise, ph = mean(calcpH), sd = sd(calcpH), se = sd/sqrt(3))
colnames(summaryRNAi)[2] <- "pval"
rnaiAll.clean$region = relevel(rnaiAll.clean$region, ref = "stem")
ggplot(rnaiAll.clean[rnaiAll.clean$region %in% c("stem", "2b", "3"),], aes(x=region, y = calcpH, fill = genotype) ) + geom_boxplot() + theme_classic() + theme(axis.text = element_text(size = 15), line = element_line(size =2 ))
