update of the news, the todolist and add of a script for Venn diagram…

… with 3 sets in the share

NEWS.md

@@ -1,5 +1,14 @@
 # DRomics (development version)
 
+NEW FEATURES
+- add of a component in the output of RNAseqdata, continuousomicdata(),  continuousanchoringdata(), microarraydata() and (data.sd, which gives, for each item, the sd of the response per condition - NA if no replicate for a condition).
+
+BUG FIXES
+- add the sample names in column names of the output of formatdata4DRomics.
+- change the default value of range4boxplot (in plot.RNAseqdata(), plot.continuousomicdata(), plot.microarraydata()) to 0 instead of 1e6 so that whiskers always go to the extrems.
+
+# DRomics 2.5-2
+
 NEW FEATURES
 
 - Put the argument dose_log_transfo by default at TRUE in functions plot.drcfit(), plotfit2pdf(), targetplot() and BMD_log_transfo at TRUE in functions bmdplot(), bmdplotwithgradient() and sensitivityplot().

man/RNAseqdata.Rd

@@ -21,7 +21,7 @@ RNAseqdata(file, backgrounddose, check = TRUE, transfo.method,
           transfo.blind = TRUE, round.counts = FALSE)
 
 \method{print}{RNAseqdata}(x, \dots)
-\method{plot}{RNAseqdata}(x, range4boxplot = 1e6, \dots)
+\method{plot}{RNAseqdata}(x, range4boxplot = 0, \dots)
 }
 
 \arguments{
@@ -62,7 +62,7 @@ using the
 
 \item{x}{An object of class \code{"RNAseqdata"}.}
 
-\item{range4boxplot}{An argument passed to boxplot(), fixed by default at 1e6 
+\item{range4boxplot}{An argument passed to boxplot(), fixed by default at 0 
 to prevent the producing of very large plot files due to many outliers. 
 Can be put at 1.5 to obtain more classical boxplots.}
 
@@ -83,7 +83,7 @@ and tranformed using functions \code{\link{rlog}} or \code{\link{vst}} of the
 }
 
 \value{ 
-   \code{RNAseqdata} returns an object of class "RNAseqdata", a list with 7 components:
+   \code{RNAseqdata} returns an object of class "RNAseqdata", a list with 9 components:
     \item{data}{ the numeric matrix of normalized and transformed
     responses of each item in each replicate
   (one line per item, one column per replicate)  }
@@ -99,7 +99,11 @@ and tranformed using functions \code{\link{rlog}} or \code{\link{vst}} of the
 
     \item{data.mean}{ the numeric matrix of mean responses of each item per dose (mean 
     of the corresponding replicates) (one line per item, one column per unique value 
-    of the dose}
+    of the dose)}
+
+    \item{data.sd}{ the numeric matrix of standard deviations of the response of each 
+    item per dose (sd of the corresponding replicates, NA if no replicate) 
+    (one line per item, one column per unique value of the dose)}
 
     \item{transfo.method}{The transformation method specified in input}
 

share/techdoc/functions2add/Venndiag3selections.R

@@ -0,0 +1,30 @@
+# Try a Venn diagram with the three selections (not so convincing)
+# To put in the vignette ?
+
+require(VennDiagram)
+microarrayfilename <- system.file("extdata", "transcripto_sample.txt", package = "DRomics")
+(o.microarray <- microarraydata(microarrayfilename, norm.method = "quantile"))
+plot(o.microarray, cex.main = 0.8, col = "green")
+
+s_quad <- itemselect(o.microarray, select.method = "quadratic", FDR = 0.01)
+s_lin <- itemselect(o.microarray, select.method = "linear", FDR = 0.01)
+s_anova <- itemselect(o.microarray, select.method = "ANOVA", FDR = 0.01)
+index_quad <- s_quad$selectindex
+index_lin <- s_lin$selectindex
+index_anova <- s_anova$selectindex
+plot(c(0,0), c(1,1), type = "n", xaxt = "n", yaxt = "n", bty = "n", xlab = "", ylab = "")
+draw.triple.venn(area1 = length(index_quad), 
+                 area2 = length(index_lin), 
+                 area3 = length(index_anova),
+                 n12 = length(which(index_quad %in% index_lin)), 
+                 n23 = length(which(index_anova %in% index_lin)), 
+                 n13 = length(which(index_quad %in% index_anova)), 
+                 n123 = length(which(index_quad %in% index_anova &
+                                       index_quad %in% index_lin)),
+                 category = c("quadratic trend test",
+                              "linear trend test",
+                              "ANOVA type test"),
+                 cat.col=c("lightblue", "purple", "orange"), 
+                 col= c("black", "black", "black"), 
+                 fill = c("lightblue", "purple", "orange"), 
+                 lty = "blank", cat.pos = c(0, 0, 0))

share/todolist.md

@@ -51,6 +51,8 @@ uniquement sur les points et pas sur l'axe des y (A)
 1. [X] Vérifier qu'on a bien indiqué partout là où on doit entrer des données
 que le séparateur de décimales devait être un point (ML ajout dans vignette et.Rd, A ajouter dans l'appli shiny 1).
 1. [ ] Vérifier le pb du download depuis chrome / machine biosphere au step 4  de l'appli shiny 1
+1.[ ] Voir si on peut ajouter les "sample names" dans le graphe des boxplot par échantillon
+1.[ ] ajouter une fonction simple qui fait une procédure d'enrichissement.
 
 ## Shorter term