CHANGES IN VERSION 1.15.02 (17 March 2020)
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+ update help page
+ rename www/imgs to www/logo: confict with www/imgs of rediant.data package.
CHANGES IN VERSION 1.15.01 (16 March 2020)
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+ Change the address of reactomeFI from "http://reactomews.oicr.on.ca:8080/" to "http://cpws.reactome.org/"
+ update ReactomeFI2018.RDS
CHANGES IN VERSION 1.11.00 (12 February 2019)
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+ Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/
CHANGES IN VERSION 1.9.07 (04 September 2018)
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+ replace DOSE::dotplot by clusterProfiler::dotplot
+ replace r_data by r_info in reports
+ not need to define genelist in r_data
+ update ReactomeFI.RDS file (version 2017)
+ update DisGeNet0918.RDS file (version September 2018), move it from wiki.ubuntu.com to github/kmezhoud
CHANGES IN VERSION 1.9.06 (30 August 2018)
------------------------
+ rm warning message for min and max functions
+ run getFreqMutData() when getListProfData() instead getCoffeeWheel_Mut(). Avoid error when loading x profiles data to workspace.
+ include Tools panel into Workspace panel.
+ update Overview image
CHANGES IN VERSION 1.9.05 (25 August 2018)
------------------------
+ r_data vs r_info ... https://radiant-rstats.github.io/docs/news.html
+ use r_info for dataset list and r_data for genes list
+ set progress bar
CHANGES IN VERSION 1.9.04 (22 August 2018)
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+ add style.css file: reduce padding-top to 0px
CHANGES IN VERSION 1.9.03 (16 August 2018)
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+ modify stop function
+ update paste gene list function
CHANGES IN VERSION 1.9.02 (16 August 2018)
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+ upload and download using Rstudio file browser
remove plot_downloader function and replace it by download_link (defined in radiant.R file)
+ add radiant_old.R file for needed functions but not longer used by radiant.data
CHANGES IN VERSION 1.9.01 (12 August 2018)
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+ replace getdata() by get_data()
+ replace factorizer() by lapply(.,factor)
CHANGES IN VERSION 1.7.05 (12 April 2018)
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+ omit importFrom clusterProfiler plot
CHANGES IN VERSION 1.7.04 (20 November 2017)
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+ export Diagrammer and viNetwork to report
+ reset image size of circomics to 1024px
CHANGES IN VERSION 1.7.03 (20 November 2017)
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+ Save network widgets as HTML and png
+ use swithc buttom for Networking Tab.
+ setwd(~)/ for windows system by setwd(Sys.getenv("R_USER"))
CHANGES IN VERSION 1.7.02 (14 November 2017)
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+ resolve conflicts renderMetabologram and renderCoffeewheel. redefine initCoffeewhell in /htmlwidges
+ report circomics widget to markdown document
+ Save static wheel as html and png (low resolution)
+ need phantomJS to catupe html widget output as png file
CHANGES IN VERSION 1.7.01 (13 November 2017)
------------------------
+ add helps to ? menu
+ change stop message
+ addResourcePath for figures
CHANGES IN VERSION 1.7.00 (30 October 2017)
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metamorphosis: bioCancer is a radiant.data extension
reduce size of package by half 14 -> 7 mb
CHANGES IN VERSION 1.5.12 (16 October 2017)
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improve Reactome_ui functions
CHANGES IN VERSION 1.5.11 (16 October 2017)
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add switch button to ui_circomics
improve circomics functions
CHANGES IN VERSION 1.5.09 (08 September 2017)
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delete commented files and figures
CHANGES IN VERSION 1.5.09 (07 September 2017)
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cleanup ui_radiant, /Rbis, /quant, /bioCancer
CHANGES IN VERSION 1.5.08 (1 September 2017)
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switchButton
CHANGES IN VERSION 1.5.07 (1 September 2017)
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data.row.names(row.names, rowsi, i) :
some row.names duplicated: 11,12,13,14 --> row.names NOT used
CHANGES IN VERSION 1.5.06 (1 September 2017)
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dplyr::mutate_each() is deprecated
dply::summarise_each() is deprecated
replace BiocStyle by prettydoc
CHANGES IN VERSION 1.5.05 (1 September 2017)
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Warning in formals(fun) : argument is not a function
Warning in body(fun) : argument is not a function
CHANGES IN VERSION 1.5.04 (02 July 2017)
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Fix setting plot size
CHANGES IN VERSION 1.5.03 (31 May 2017)
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Change the color rang of Circular layout plot as in standards
CHANGES IN VERSION 1.5.02 (30 May 2017)
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update Correlation Methods
CHANGES IN VERSION 1.5.01 (29 May 2017)
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replace .libPath() by path.package('bioCancer') in portal.R file
CHANGES IN VERSION 1.0.16 (03 January 2017)
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o update documents
CHANGES IN VERSION 1.0.13 (28 December 2016)
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o Reactome tab update
CHANGES IN VERSION 1.0.12 (27 December 2016)
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o Simplify genes classification
CHANGES IN VERSION 1.0.10 (25 December 2016)
------------------------
o clarify interface: Pipeline Overview
o remove Cluster and Factor Menus
CHANGES IN VERSION 1.0.07 (14 December 2016)
------------------------
o add argument to whichGeneLits(input$GeneListID)
o Use the SUM of mutation cases and NOT SUM/TOTAL_SUM (ratio)
o replace dplyr::add_rownames() by tibble::rownames_to_column()
o replace stopping process (stop function) by warning message. stop function disconnect session in server version.
o resolve error message when Gene list is empty (paste empty gene list).
getListProfData, getFreqMutData, ProfData, MutData, Classifier, geNetClassifier, Circomics_ui, getCircomics, Reactome_ui.
o Make it possible to get Circomics only for one study. Essentially resolve data structure in processing of mutation data frame.
CHANGES IN VERSION 1.0.03 (29 Septembre 2016)
------------------------
o update pivotr from radiant.data
CHANGES IN VERSION 1.0.02 (29 Septembre 2016)
------------------------
o replace dplyr::add_rownames() by tibble::rownames_to_column()
CHANGES IN VERSION 1.0.01 (29 Septembre 2016)
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o rm "id=" from navbarMenu - shiny update
CHANGES IN VERSION 1.0.0 (07 July 2016)
------------------------
o built vignette with knitr
o modify whichGeneList(GeneListLabel)
resolve difference between bioCancer server and package
FIRST RELEASE
o Package released
o Omit R/code menu: request shinyAce (>=0.2.1)
- Omit help_and_report function
o Various issues request DT (>=0.1.39)
- Omit Show Plot in Pivot sidebar menu
- Can not download/Store correctly filtered table in Handle/View
PERSPECTIVE
o Release R 3.4 import(shiny, except= c("dataTableOutput", "renderDataTable"))
o use DisGeNet server despite /extdata/disGeNet file (DONE Not Working)
o clusterProfiler GMT file:
http://www.r-bloggers.com/go-analysis-using-clusterprofiler/
o gene classification using rpart,ggplot2, ggtree:
http://guangchuangyu.github.io/2016/01/annotate-a-phylogenetic-tree-with-insets/
o Specify the range of mutation frequency in circos plot [Min, Max]