hist_limits

R/rawpHist.R

@@ -16,7 +16,7 @@ rawpHist <- function(result, outfile=FALSE){
   for (name in names(result)){
     result.name <- result[[name]]
     p[[name]] <- ggplot(data=result.name, aes(x=.data$pvalue)) +
-      geom_histogram(binwidth=0.02) +
+      geom_histogram(color="white", breaks=seq(0, 1, by=0.025)) +
       scale_y_continuous(expand=expand_scale(mult=c(0.01, 0.05))) +
       xlab("Raw p-value") +
       ylab("Frequency") +

inst/Report_ChIPuanaR.Rmd

@@ -22,10 +22,10 @@ library(knitr)
 library(kableExtra)
 library(ChIPuanaR)
 ### INPUTS
-source("config.R")
-data <- read.table(file = file, header=TRUE)
-counts <- as.matrix(data[,-c(1:6)])
-rownames(counts) <- data[,1]
+# source("config.R")
+# data <- read.table(file = file, header=TRUE)
+# counts <- as.matrix(data[,-c(1:6)])
+# rownames(counts) <- data[,1]
 ```
 
 ```{r echo=FALSE, results="asis", results="hide", message=FALSE}
@@ -70,8 +70,8 @@ if (method=="Limma") {
 }
 # Export result table
 for (name in names(resAnDif$results)){
-  write.table(resAnDif$results[name], file=paste0(name,"_resAnDif.txt"), sep="\t", 
-              row.names=TRUE, col.names=TRUE, dec=".", quote=FALSE)
+  write.table(resAnDif$results[[name]], file=paste0(name, "_resAnDif.txt"), sep="\t", 
+              row.names=TRUE, col.names=NA, dec=".", quote=FALSE)
 }
 ```
 
@@ -84,6 +84,7 @@ The count data files and associated biological conditions are listed in the foll
 ```{r , echo=FALSE, results="asis"}
 # Echo design
 design <- data.frame(Conditions, row.names = colnames(counts))
+if (!is.null(batch)) design$batch <- batch
 kable(design, caption = "Table 1: Data files and associated biological conditions",format = "html") %>%
   kable_styling(c("striped", "bordered", "responsive"), font_size = 14) %>%
   column_spec(1, bold = T)
@@ -150,7 +151,7 @@ PCAPlot(counts.trans = counts.trans, conditions = Conditions, outfile = FALSE)
 
 ```{r , echo=FALSE, results="asis"}
 if (!is.null(batch)){
-  cat("For the statistical analysis, we need to take into account the effect of the ", batch, " parameter. Statistical models and tests will thus be adjusted on it.\n")
+  cat("For the statistical analysis, we need to take into account the effect of the batch parameter. Statistical models and tests will thus be adjusted on it.\n")
 }
 ```