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make test experiment

library(rosettR)

meta <- metaTemplate(letters[1:4], treatments=c("control", "osmotic"),
                     timepoints=c(11, 14, 16, 18), nrepeats=3)
rosettR:::newExperiment("pkg/inst/examples/rosettrTest", meta)

for(i in meta$timepoints)
    file.copy(
        sprintf("EXP001_Daniel/D%d/plate%03d.jpg", i, 1:6),
        sprintf("pkg/inst/examples/rosettrTest/D%d/", i)
        )

file.copy("pkg/inst/examples/rosettrTest.zip",
          file.path(.libPaths()[1], "rosettR/examples/rosettrTest.zip"),
          overwrite=TRUE)

makeTestExperiment()

create a new experiment and get the sowing report

library(rosettR)
file.copy("pkg/inst/templates/template.html",
          file.path(.libPaths()[1], "rosettR/templates"), overwrite=TRUE)

file.copy("pkg/inst/reports/layout.Rmd",
          file.path(.libPaths()[1], "rosettR/reports"), overwrite=TRUE)

makeReport("rosettrTest", "layout")

raw image gallery

  • State “DONE” from “TODO” [2015-11-05 Thu 22:49]
file.copy("pkg/inst/reports/overview.Rmd",
          file.path(.libPaths()[1], "rosettR/reports"), overwrite=TRUE)
file.copy("pkg/inst/templates/overview.html",
          file.path(.libPaths()[1], "rosettR/templates"), overwrite=TRUE)
makeReport("rosettrTest", "overview")

analyze the images

  • State “DONE” from “TODO” [2015-11-08 Sun 12:59]
processPlateExperiment("rosettrTest")

qc report

file.copy("pkg/inst/reports/quality-check.Rmd",
          file.path(.libPaths()[1], "rosettR/reports"), overwrite=TRUE)

makeReport("rosettrTest", "quality-check")

test removing some boxes and redo

  • State “DONE” from “TODO” [2015-11-11 Wed 21:30]

works now, see example reprocessPlateImages

plus document this in qc report

prettify reports with css and stuff

  • State “DONE” from “TODO” [2015-11-12 Thu 14:22]

http://www.r-bloggers.com/fast-track-publishing-using-knitr-the-setup-using-rprofile-with-custom-css-some-html-goodies-part-ii/

easy, use templates

file.copy("pkg/inst/templates/template.html",
          file.path(.libPaths()[1], "rosettR/templates"), overwrite=TRUE)

makeReport("rosettrTest", "quality-check", "qc")

make fancy image gallery

  • State “DONE” from “TODO” [2015-11-12 Thu 20:50]

use DT where needed

  • State “DONE” from “TODO” [2015-11-12 Thu 23:24]
  • the anova table output

R cmd check…

  • State “DONE” from “TODO” [2015-11-16 Mon 22:04]

write first vignette and then send to publication approval

  • State “DONE” from “TODO” [2015-11-22 Sun 10:27]

fix main vignette

  • State “DONE” from “TODO” [2015-11-22 Sun 15:54]

harmonize words

  • State “DONE” from “TODO” [2015-11-22 Sun 13:35]
  • genotype not germplasm
  • box not well
  • blocks not repeats

CANCELED copy run.R file?

  • State “CANCELED” from “TODO” [2015-11-22 Sun 10:28]
    never worked well in practice anyway

confirm multi-core working

  • State “DONE” from “TODO” [2015-11-22 Sun 18:58]

add unit tests

  • State “DONE” from “TODO” [2015-11-22 Sun 21:12]

test by re-analyzing some old experiment

  • State “DONE” from “TODO” [2015-12-06 Sun 11:34]

EXP128_SALK_BS works well

filipas points

  • State “DONE” from “TODO” [2016-01-09 Sat 20:24]

when i open the sowing summary, the control

  • State “DONE” from “STARTED” [2016-01-09 Sat 20:13]
  • State “STARTED” from “TODO” [2016-01-09 Sat 12:59]

and osmotic stress tabs are defined as date, i guess this a problem of my excel but not sure if we can fix this somehow? (see excel attached)

the plates in the example are not correctly

  • State “DONE” from “STARTED” [2016-01-09 Sat 20:24]
  • State “STARTED” from “TODO” [2016-01-09 Sat 16:15]

centered, is this a problem? (only D11)

the plates provided are

  • State “DONE” from “STARTED” [2016-01-09 Sat 20:24]
  • State “STARTED” from “TODO” [2016-01-09 Sat 19:16]

already renamed, so could not test if the renaming works.

the make report overview opens

  • State “DONE” from “TODO” [2016-01-09 Sat 19:36]

an html with all the plates, but with no reference - only when we click on the plate we see the details. would be handy to have some kind of grid or explanation on the order of the plates in the html (as far as i understood, its days on the x axis and plate number on the y axis, right?)

I could not understand immediatelly

  • State “DONE” from “TODO” [2016-01-09 Sat 19:57]

what i had to do with the calibrateScale(pathToExperiment)… first it said choose the distance to indicate [default=80mm] but i had to press enter, and only then something appeared to click on the plates. The first time i just typed 80mm and nothing happened. maybe a better explanation there is needed.

CANCELED after analysis i had this error (below plate)

  • State “CANCELED” from “TODO” [2016-01-09 Sat 19:58]
    due to calibration mistake

so I could not proceed any further…! could it be because i could not properly set the scale in the plate? see how i made it here - I did not type

unzip(system.file(“examples/rosettrTestResults.zip”, package=”rosettR”), exdir=”.”)

because i pasted the pictures in the folders, so I assume i did not have to do this.

CANCELED add zygosity stat report

  • State “CANCELED” from “DONE” [2016-01-09 Sat 21:09]
    not really needed.
  • State “DONE” from “TODO” [2016-01-09 Sat 21:09]

make dateTaken not crash

  • State “DONE” from “TODO” [2016-01-09 Sat 20:53]

on jpegs without exif an tag

library(rosettR)
## crashes R
dateTaken(system.file("examples/empty-qc.jpg", package="rosettR"))

Testing

rosettrTest

reportFiles <- list.files("pkg/inst/reports", pattern=".*Rmd$", full.names=TRUE)
lapply(reportFiles, file.copy,
       to=file.path(.libPaths()[1], "rosettR/reports"),
       overwrite=TRUE)

library(rosettR)
makeTestExperiment()
makeReport("rosettrTest", "layout")
makeReport("rosettrTest", "overview")
processPlateExperiment("rosettrTest")
makeReport("rosettrTest", "quality-check")
makeReport("rosettrTest", "compare-areas")

Test a single image

library(EBImage)
library(rosettR)
file <- "c:/git/rosettr/diff.jpg"

file <- "c:/git/rosettr/rosettrTest/D11/plate004.jpg"

file <- "c:/git/rosettr/pkg/inst/examples/rosettrTest/D11/plate001.jpg"

meta <- metaTemplate(letters[1:4], LETTERS[1:2])
df <- analyzeImage(file, meta$griddf, 7.538, 20, 6, 75, verbose=TRUE,
                   checkrotation=TRUE)

display(readImage(df$qc_picture[1]), method="raster")

growth curves in the qc report

  • State “DONE” from “TODO” [2016-01-10 Sun 11:26]

add readme

  • State “DONE” from “TODO” [2016-01-10 Sun 15:03]

io website

  • State “DONE” from “TODO” [2016-01-11 Mon 09:16]

add link to vignette

  • State “DONE” from “TODO” [2016-01-12 Tue 09:14]

add builds

  • State “DONE” from “TODO” [2016-03-15 Tue 12:13]

https://www.dropbox.com/s/i36ypkm4wihfcsu/rosettR_0.0.5.tar.gz?dl=0 https://www.dropbox.com/s/ljlwiza85zoy8b8/rosettR_0.0.5.zip?dl=0

flowcharts

  • State “DONE” from “TODO” [2016-03-15 Tue 12:13]

*

add auto links to new builds

continue test experiment