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.Rapp.history
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hist(htm@wellSummary$MeanRatioScore__ANOVA__centroCellsDivAllCells__weighted_mean_of_images)
hist(htm@wellSummary$minusMeanCtrl__ANOVA__centroCellsDivAllCells__weighted_mean_of_images)
log2(10)
summary(htm@wellSummary$wellscore__centroCellsDivAllCells__weighted_mean_of_images)
hist(htm@wellSummary$wellscore__centroCellsDivAllCells__weighted_mean_of_images)
plot(htm@wellSummary$wellscore__centroCellsDivAllCells__weighted_mean_of_images)
plot(htm@wellSummary$logScore__ANOVA__centroCellsDivAllCells__weighted_mean_of_images)
traceback()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
colnames(htm@wellSummary)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
colnames(htm@wellSummary)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
colnames(htm@wellSummary)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
is.numeric(c(1,Inf,2))
which(is.numeric(c(1,Inf,2)))
Inf
is.numeric(Inf)
??is.numeric
?is.numeric
?Inf
is.finite(c(1,Inf,-Inf,NA))
a = c(1,Inf,-Inf,NA)
is.finite(a)
aOK = subset(a,is.finite(a))
aOK
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
1
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
colnames(htm@wellSummary)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
log2(20)-log2(10)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
traceback()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htm@wellSummary$wellQC[1, "wellQC"]
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
2^(1.825763)
2^(-1.825763)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
2^(-1.825763)
x=-1.825763
sign(x)*2^abs(x)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
?subset
warnings()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
warnings()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
warnings()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
traceback()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
edit(htm@data)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htm@settings@columns$experiment
htm@settings@columns$treatment
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmGetVectorSettings(htm,"treatmentSelectionForPlotting")
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmJitterplot(htm,"","")
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmGetListSetting("visualisation","jitterPlot_colorizeTreatments_TF")
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
?vector
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htm@data$centroCellsDivAllCells = htm@data$Count_CentroCells / htm@data$Count_CentroCells
r <- htmTreatmentSummary(htm)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
?gfile
?path
path = gfile("Save as...", type="save", initialfilename = paste0(htmGetListSetting("statistics","measurement"),".csv"))
path = gfile("Save as...", type="save", initialfilename = paste0("TreatmentSummary--"htmGetListSetting("statistics","measurement"),".csv"))
path = gfile("Save as...", type="save", initialfilename = paste0("TreatmentSummary--",htmGetListSetting("statistics","measurement"),".csv"))
path
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r <- htmTreatmentSummary(htm)
?switch
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r <- htmTreatmentSummary(htm)
edit(r)
htm
htm@log
htmAddLog("adasdas")
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmAddLog("adasdas")
htm@log
cat(htm@log)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmClearLog
htmClearLog()
htm@log
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
cat(htm@log)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
cat(htm@log)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
cat(htm@log)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
edit(r)
r2 <- r(order(r$ANOVA_pValue),)
r2 <- r[order(r$ANOVA_pValue),]
edit(r2)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
cat(htm@log)
path = gfile("Save as...", type="save", initialfilename = paste0("TreatmentSummary--",htmGetListSetting("statistics","measurement"),".csv"))#
htmSaveDataTable(htm, "treatmentSummary", path)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
path = gfile("Save as...", type="save", initialfilename = paste0("TreatmentSummary--",htmGetListSetting("statistics","measurement"),".csv"))#
htmSaveDataTable(htm, "treatmentSummary", path)
traceback()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
edit(htm@treatmentSummary)
htm@data$centroCellsDivAllCells = htm@data$Count_CentroCells / htm@data$Count_Cells
head(htm@data$centroCellsDivAllCells)
cat(htm@log)
htmAddLog("aaa")
cat(htm@log)
htmAddLog(htm@wellSummary$treatment[1])
cat(htm@log)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
cat(htm@log)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmPrintLog()
cat(htm@log)
cat(htm@Log)
cat(htm@log)
htmClearLog()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmPrintLog()
cat(htm@log)
htmPrintLog()
length(htmPrintLog())
htmClearLog()
htmPrintLog()
htmAddLog("asss")
htmPrintLog()
htmPrintLog("SAdasd")
htmAddLog("assasdadss")
htmPrintLog("SAdasd")
htmPrintLog()
htmClearLog()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmPrintLog()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmClearLog()
htmPrintLog()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htm@log
cat(htm@log)
htmClearLog()
htmShowLog9)
htmShowLog())
htmShowLog()
htmPrintLog()
htmAddLog("");htmAddLog("Experiments:")
htmPrintLog()
htmAddLog("");htmAddLog("Experiments:")
htmPrintLog()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r <- htmTreatmentSummary(htm)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r <- htmTreatmentSummary(htm)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r <- htmTreatmentSummary(htm)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r <- htmTreatmentSummary(htm)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htm@data$CentroCells_div_AllCells = htm@data$Count_CentroCells / htm@data$Count_Cells
head(htm@data$CentroCells_div_AllCells)
htmGetListSetting("statistics","normalisationMethod")
htmGetListSetting("statistics","transformation")
dev.copy(png,'myplot.png')
pwd
getwd()
?dev.copy
?jpeg
png(filename="/Users/tischi/Dropbox/R/test.png")
?png
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r<-htmTreatmentSummary(htm)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r<-htmTreatmentSummary(htm)
hist(htm@data$CentroCells_div_AllCells)
dev.off()
hist(htm@data$CentroCells_div_AllCells)
png('/Users/tischi/Dropbox/test.png')
hist(htm@data$CentroCells_div_AllCells)
dev.off()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r<-htmTreatmentSummary(htm)
dev.off()
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r<-htmTreatmentSummary(htm)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r<-htmTreatmentSummary(htm)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r<-htmTreatmentSummary(htm)
?pdf
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
r<-htmTreatmentSummary(htm)
colnames(htm@wellSummary)
hist(htm$wellSummary$minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images)
hist(htm@wellSummary$minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images)
dev.off()
hist(htm@wellSummary$minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmHisto(minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images, datatype="wells", treatmentSubset="s229174--Scramble")
htmHisto("minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images", datatype="wells", treatmentSubset="s229174--Scramble")
htmHisto("minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images", datatype="wells")
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmHisto("minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images", datatype="wells", treatmentSubset="s229174--Scramble")
?hist
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmHisto("minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images", datatype="wells", treatmentSubset="s229174--Scramble")
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
htmHisto("minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images", datatype="wells", treatmentSubset="s229174--Scramble", save2file=T)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
colnames(htm@wellSummary)
hist(htm@wellSummary$minusMeanCtrl__CentroCells_div_AllCells__weighted_mean_of_images)
qqplot(htm@wellSummary$minusMeanCtrl__CentroCells_div_AllCells__weighted_mean_of_images)
?qqplot
qqnorm(htm@wellSummary$minusMeanCtrl__CentroCells_div_AllCells__weighted_mean_of_images)
colnames(htm@wellSummary)
qqnorm(htm@wellSummary$minusMeanCtrl__log2__CentroCells_div_AllCells__weighted_mean_of_images)
htmGetVectorSettings(htm, "treatmentSelectionForPlotting")
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T);
colnames(htm@data)
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T)
htm@data$plate = "myPlate"
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T)
htm@data$subpos = 1
source("/Users/tischi/Dropbox/R/HTM/install.R", chdir=T)
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");
sort(unique(htm@data[[htm@settings@columns$experiment]]))
htm@settings@columns$experiment
c("a",NULL)
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");
traceback()
treatments
experiments
!is.null(htm@settings@columns$experiment)
htm@settings@columns$experiment
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");
?title
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");
path = "/Users/tischi/Dropbox/R/HTM/HTM_Explorer/HTM_Explorer";setwd(path);source("run.R");