Changes in version 1.11.3 (2018-01-19): MODIFICATIONS o Added select all buttons to other marker related plots o Changed scaling and centering options to drop-down menus o Updated maintainer emails o Added transparency option to expression level plot points so points dont obscure each other too much. Point size can be adjusted to improve visibility as well BUG FIXES o Fixed handling of global scaling so that expression values don't fall outside the limits for the colour palette in the shiny color plots o Improved the outlier removal code in color plots to be more robust for various marker expression patterns o Shifted a line that compares fixedNum argument against the number of events so that it doesn't break when the 'min' mergeMethod sets fixedNum to NULL Changes in version 1.11.2 (2017-12-15): MODIFICATIONS TO EXPRESSION LEVEL SCATTERPLOT o Marker selection changed to selectize style, choices "All Markers" and "All Markers (scaled)" removed. o Added checkbox option to scale the legend and dot colours locally/globally o Added checkbox option to scale and center expression values o Added actionButton to select all markers (will update selectize choices to select all) o Added actionButton to update plot after changing marker selection (otherwise will update with each marker added/removed) BUG FIXES o Changed limits of scatterplot scale from min-max to min-98th percentile to account for rare extreme outliers. Changes in version 1.11.1 (2017-11-06): MODIFICATIONS o Added a select/deselect all checkbox to the sample selection panel for ease of selection. o Added FlowSOM option and options to specify k for FlowSOM and Rphenograph in cytofkit_GUI. o Added a popup dialog to cytofkit_GUI that warns if more than 10,000 cells are being run with DensVM or isomap BUG FIXES o Switched the treetype used for nn2 from bd to kd, as bd was causing problems in Phenograph clustering. Changes in version 1.10.0 (2017-11-01): BIOCONDUCTOR 3.6 RELEASE o Contains all modifications and fixes from 1.8.2 to 1.9.5 Changes in version 1.9.5 (2017-10-23): MODIFICATIONS o Standardise plot scales across samples in shiny App BUG FIXES o Fixed an issue with Phenograph failing if sampling with replacement was done. Now cytofkit tests if any FCS files have less events than specified in fixedNum argument. Changes in version 1.9.4 (2017-09-27): MODIFICATIONS o Added function, cytof_clustermtrx(), to obtain marker expression values for cells in a given cluster. o Included cytof_clustermtrx() into main cytofkit function. o Cluster ID integers saved to fcs files as additional channels. BUG FIXES o Quick fix on FCS saving. Changes in version 1.9.3 (2017-09-27): MODIFICATIONS o Added arguments to cytofkit() and cytof_cluster() to allow user to set a seed, for reproducible results. BUG FIXES o Users can now save .fcs from shiny output after renaming samples. Changes in version 1.9.2 (2017-09-11): MODIFICATIONS o Added save data options for shiny app. Now you can select any combination of .fcs, .csv, and .rdata outputs. o cytofkitShinyAPP() uses code from cytofkit_shinyAPP.R for visualisation on local machines, while ui.R and server.R can be used separately to host the app on servers. BUG FIXES o Fixed some issues with viewing and downloading the marker heatmap in the shiny app o Fixed an inconsistency where expression data used for clustering was not selective for markers used for dimension reduction Changes in version 1.8.3 (2017-09-06): BUG FIXES o cytofkitShinyAPP file size cap consistently set to 100mb Changes in version 1.8.2 (2017-07-24): NEW FEATURES o cytofkitShinyAPP function now takes RData as argument to skip reuploading RData o While choosing selected markers for dimension reduction and clustering, all markers can be visualised in the shiny app o Added a "reset" button to ShinyApp to clear the session and start over o Added Server file select button to allow browsing server files MODIFICATIONS o Combined both cytofkitShinyAPP functions into one o ShinyApp uses actionButton for download instead of a downloadHandler o ShinyApp displays what .RData is loaded into its reactive data o ShinyApp lists markers in alphabetical order o Marker selection done at dimensionality reduction stage rather than at raw data transformation, to allow all expression data to be visualised at later stages o Updated examples and vignettes to account for updates done o Updated maintainer email address Changes in version 1.8.1 (2017-04-26): NEW FEATURES o fixed documentation warning for function cytofkitShinyAPP2 o updated my maintainer email address Changes in version 1.6.6 (2017-04-11): NEW FEATURES o add fixedLogicle transformation option on the GUI, with window popup to allow specifing the w, t, m, a parameters for logicle transformation. o add openShinyAPP (boolean parameter) option in cytofkit main function, which can open shinyAPP once the analysis was done and automatically load the result object into the shinyAPP for exploration. o add cytofkitShinyAPP2 function which can take cytofkit analysis_results (either file name of R object) as input and automatically load to shinyAPP once launched. Changes in version 1.6.5 (2017-03-27): MODIFICATION o debug that FlowSOM_k doesn't work in cytofkit main function Changes in version 1.6.4 (2017-03-17): MODIFICATION o in the shiny server code change function call of c in do.call to base::c Changes in version 1.6.3 (2017-03-16): MODIFICATION o debug the FSC|SSC channel processing error Changes in version 1.6.2 (2017-03-08): NEW FEATURES o add default linear transformation to FSC and SSC channels o add support for PDF figure download on shinyAPP, update the side panel to be tab dependent o add new color palatte in heatmap (greenred and spectral) and level plot (spectral) o Add cluster filter in cluster plot on shinyAPP o Allow multiple annotation for same cluster (specify cluster_annotation name) on shinyAPP o Allow color selection for each cluster on shinyAPP o Allow modification of the marker name on shinyAPP Changes in version 1.6.1 (2016-10-27): MODIFICATION o updated colorPalette options in cytof_colorPlot function, also the Shiny APP, added spectral. o debugged rowname conflication when regroup the samples in shinyAPP, now only use global ID, discarded the local cell ID, which avoid the dumplicate rownames conflication but results in failure in saving new FCS files. Changes in version 1.4.10 (2016-10-05): MODIFICATION o corrected the citation title o added cluster filter in rateChange line plot in ShinyAPP o debugged the error of loading back exported RData file o updated the saving button, make it more robust. If cannot find FCS path, then doesn't save new FCS files o added progression indicator in shinyAPP Changes in version 1.4.9 (2016-09-27): MODIFICATION o debug when w is negative in autoLgcl transformation, convert to logicle transformation in this case o modify the cytof_writeResults function to make it more robust, with several more saving options. o set autoLgcl as the default transformation method. NEW FEATURES o big updates on the layout of shinyAPP, functions categorized into four panels ("cluster", "marker", "sample", "progression") o added "group samples" function to relabel and group samples in sample panel o added subset precentage change plot in sample panel o added case checking of Nan of w in autoLgcl function o Added cluster filtering and cluster table on shinyAPP diffusionmap set up page o Added combined view of marker expression patten on scatter plot and marker expression trend on subset progression o Added stack density plot in Marker Plot o Added cluster annotation (Label Clusters) in Marker Plot o add none option for transformation method to support FCS files with data already transformed o add "Seperate Plot by Samples" on side panel, remove option "Label Samples by Shapes" o make sample filter works on subset progression panel, support plot labeld on grid plot o add cytofkit plos computational biology paper in CITATION Changes in version 1.4.8 (2016-07-08): MODIFICATION o Adjusted the windown width and height of getParameters_GUI() to fit long name of FCM data o debugged, set full.names = TRUE in getParameters_GUI() when fcsFile == NULL Changes in version 1.4.7 (2016-07-04): MODIFICATION o Concised the autoLgcl function Changes in version 1.4.6 (2016-06-14): MODIFICATION o concised the title in vignette, tiny modification o added missed halo variable in ClusterX o added transformation=FALSE in calling read.FCS function to avoid unexpected transformation for flow cytometry data. o changed cast from reshap to dcast from reshap2 in function cytof_writeResults o added projectName, rawFCSdir, resultDir entries in analysis_results object o modified parameters for cytof_writeResults, only need analysis_results object o replaced parameter uniformClusterSize in cytofkit to clusterSampleSize NEW FEATURES o redesigned shiny APP, big updates on subset progression tab, support FlowSOM and Diffusion map running. Added save buttion. o rewrited most of the codes in function cytof_progression o added diffusionmap in cytof_progression, updated on GUI o added reverseOrder option in cytof_progressionPlot function o added clusterLabelSize option in cytof_progressionPlot function o added segmentSize option in cytof_progressionPlot function o added cluster filetering and addClusterLabel option in cytof_progressionPlot o added fixCoord option to function cytof_clusterPlot o added distMethod option in cytof_progression function o added distance calculation options in cytof_dimReduction o added tsneSeed in cytof_dimReduction for reproducible t-SNE results o added cytof_clusterStat and cytof_colorPlot function in cytof_postProcess o added a button on GUI to open the resultDir once the cytof_writeResults was done, cross platform. Changes in version 1.4.5 (2016-06-12): MODIFICATION o Solved examples runing bug on 1.4.4 Changes in version 1.4.4 (2016-05-25): MODIFICATION o use match.arg together with match to concise the codes o renamed function auto_lgcl to autoLgcl o renamed function densVM to DensVM o renamed function distMethod to isomap_distMethod, more informative o changed usage of apply to rowSums in ClusterX, much faster o ClusterX use RANN::nn2 to speedup core/halo detection o apply binary search to speedup estimateDc in ClusterX, sample size is set to 5000 by default o Modified the vignettes, applied BiocStyle format o debugged the dumplicate name confliction in cytof_addToFCS by modify to_add_i[[addColName]] the to_add_i[[j]] NEW FEATURES o added function cytofAsinh for CyTOF data transformation o added transformMethod on the GUI, two options include cytofAsinh and fcmLgcl o added FlowSOM clustering method o added visualizaiton option of runFlowSOM, DensityPlot, DotPlot, ColorBySample in shinyAPP o added sampleLabel option in function cytof_clusterPlot o added cex_row_label and cex_col_label options in function cytof_heatmap Changes in version 1.4.3 (2016-05-16): MODIFICATION o Dubugged dimReduction selection error Changes in version 1.2.3 (2016-04-04): MODIFICATION o updated the shiny APP, heatmap scale, plot with selection of all markers o output with a copy of expression with all markers o updated the shiny APP, heatmap scale, plot with selection of all markers o output with a copy of expression with all markers Changes in version 1.2.2 (2016-03-04): MODIFICATION o removed comp parameter in cytofkit-function o changed parameter comp to ifCompensation in cytofkit-function o adjusted the order of parameters in cytofkit-funciton Changes in version 1.2.1 (2015-12-30): MODIFICATION o change main function cytof_tsne_densvm to cytofkit, correspondingly change cytof_tsne_densvm_GUI to cytofkit_GUI o change fcs_lgcl to cytof_exprsExtract o change fcs_lgcl_merge to cytof_exprsMerge o change densVM_cluster to cytof_cluster o change sign_auto to auto_lgcl o updated the GUI o updated vignettes NEW FEATURES o redesigned the pipeline with a general framework o added new clustering methods ClusterX and Rphenograph o added progression estimation using ISOMAP o added a shiny APP to access the results interactively Changes in version 1.0.0: MODIFICATION o renamed package name from sidap to cytofkit