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