[maftools.ui.sections] order = ["readfiles", "getFields", "getSampleSummary", "plotmafSummary", "oncoplot_default", "oncoplot_with_cnv", "oncoplot_advanced", "plotTiTv", "lollipopPlot2", "tcgaCompare", "plotVaf", "somaticInteractions", "oncostrip", "plotEnrichmentResults", "plotClusters"] [maftools.ui.sections.ui_basic] readfiles = "title = 'Input files', status = 'primary', width = 12, collapsed = FALSE, collapsible = TRUE" getFields = "title = 'Output of maftools fields summary', status = 'primary', width = 12, collapsed = TRUE, collapsible = TRUE" getSampleSummary = "title = 'Output of maftools sample summary', status = 'primary', width = 12, collapsed = TRUE, collapsible = TRUE" getGeneSummary = "title = 'Output of maftools gene summary', status = 'primary', width = 12, collapsed = TRUE, collapsible = TRUE" getClinicalData = "title = 'Output of maftools clinical data summary', status = 'primary', width = 12, collapsed = TRUE, collapsible = TRUE" plotmafSummary = "title = 'Output of maftools MAF summary', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" oncoplot_default = "title = 'Output of maftools oncoplots', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" oncoplot_with_cnv = "title = 'Output of maftools oncoplots with copy number data', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" oncoplot_advanced = "title = 'Output of maftools oncoplots with advanced', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" plotTiTv = "title = 'Output of maftools transition and transversions', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" lollipopPlot = "title = 'Output of maftools Lollipop plots for amino acid changes', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" lollipopPlot2 = "title = 'Output of maftools Lollipop2 plots for amino acid changes', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" tcgaCompare = "title = 'Output of maftools comparing mutation load', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" plotVaf = "title = 'Output of maftools VAF boxplot', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" gisticChromPlot = "title = 'Output of maftools gistic genome plot', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" gisticBubblePlot = "title = 'Output of maftools gistic bubble plot', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" gisticOncoPlot = "title = 'Output of maftools gistic oncoplot plot', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" somaticInteractions = "title = 'Output of maftools somatic interactions', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" oncostrip = "title = 'Output of maftools somatic interactions (oncostrip)', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" plotOncodrive = "title = 'Output of maftools driver based on positional clustering', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" mafSurvival = "title = 'Output of maftools Survival', status = 'primary', width = 12, collapsed = TRUE, collapsible = TRUE" plotEnrichmentResults = "title = 'Output of maftools Clinical enrichment analysis', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" plotClusters = "title = 'Output of maftools heterogeneity analysis', status = 'primary', width = 12, collapsed = TRUE, height='auto', collapsible = TRUE" [maftools.paramters.readfiles] # For reading annovarR shiny APP maftools tool input files section_type = "input" rcmd_last = """ laml = read.maf(maf = laml_maf, clinicalData = laml_clin) laml.plus.gistic = read.maf(maf = laml_maf, gisticAllLesionsFile = all_lesions, gisticAmpGenesFile = amp_genes, gisticDelGenesFile = del_genes, gisticScoresFile = scores_gis, isTCGA = is_tcga) laml.gistic = readGistic(gisticAllLesionsFile = all_lesions, gisticAmpGenesFile = amp_genes, gisticDelGenesFile = del_genes, gisticScoresFile = scores_gis, isTCGA = is_tcga) primary_maf = read.maf(maf = primary_maf) relapse_maf = read.maf(maf = relapse_maf) """ progressbar_message = "Reading related MAF and other files." render_id = "maftools_readfiles" #!!!!! input_ui_order required related section input_ui_order = ["single_input", "cnv_input", "comparsion_input", "other_params", "start_analysis"] [maftools.paramters.readfiles.input.single_input] title = "Single sample anlayais:" title_control = "class = 'input-section-p'" varname = ["laml_maf", "laml_clin", "laml_mutsig"] input_id = ["input_maf", "input_clin", "input_mutsig"] type = ["shiny::selectInput", "shiny::selectInput", "shiny::selectInput"] label = ["MAF file (laml_maf)", "Clincal annotation file (laml_clin)", "MutSig reusults (laml_mutsig)"] [maftools.paramters.readfiles.input.single_input.choices] laml_maf = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(maf)', full.names = TRUE), featch_files(c('maf', 'maf.gz'))$file_path)}" laml_clin = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(txt)|(tsv)', full.names = TRUE), featch_files(c('tsv', 'txt', 'txt.gz', 'tsv.gz'))$file_path)}" laml_mutsig = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(txt)|(tsv)', full.names = TRUE), featch_files(c('tsv', 'txt', 'txt.gz', 'tsv.gz'))$file_path)}" [maftools.paramters.readfiles.input.single_input.selected] laml_maf = "@>@system.file('extdata', 'tcga_laml.maf.gz', package = 'maftools')@<@" laml_clin = "@>@system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools')@<@" laml_mutsig = "@>@system.file('extdata', 'LAML_sig_genes.txt.gz', package = 'maftools')@<@" [maftools.paramters.readfiles.input.cnv_input] title = "CNV related analyais:" title_control = "class = 'input-section-p'" varname = ["all_lesions", "amp_genes", "del_genes", "scores_gis"] input_id = ["input_gistic_all_lesions", "input_gistic_amp", "input_gistic_del", "input_gistic_score"] type = ["shiny::selectInput", "shiny::selectInput", "shiny::selectInput", "shiny::selectInput"] label = ["Gistic all lesions file (all_lesions):", "Gistic amp genes file (amp_genes)", "Gistic del genes file (del_genes)", "Gistic score file (scores_gis)"] [maftools.paramters.readfiles.input.cnv_input.choices] all_lesions = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(txt)|(tsv)', full.names = TRUE), featch_files(c('txt', 'txt.gz'))$file_path)}" amp_genes = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(txt)|(tsv)', full.names = TRUE), featch_files(c('txt', 'txt.gz'))$file_path)}" del_genes = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(txt)|(tsv)', full.names = TRUE), featch_files(c('txt', 'txt.gz'))$file_path)}" scores_gis = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(gistic)', full.names = TRUE), featch_files(c('txt', 'txt.gz', 'gistic'))$file_path)}" [maftools.paramters.readfiles.input.cnv_input.selected] all_lesions = "@>@system.file('extdata', 'all_lesions.conf_99.txt', package = 'maftools')@<@" amp_genes = "@>@system.file('extdata', 'amp_genes.conf_99.txt', package = 'maftools')@<@" del_genes = "@>@system.file('extdata', 'del_genes.conf_99.txt', package = 'maftools')@<@" scores_gis = "@>@system.file('extdata', 'scores.gistic', package = 'maftools')@<@" [maftools.paramters.readfiles.input.comparsion_input] title = "Comparsion between different cohort:" title_control = "class = 'input-section-p'" varname = ["primary_maf", "relapse_maf"] input_id = ["input_primary_maf", "input_relapse_maf"] type = ["shiny::selectInput", "shiny::selectInput"] label = ["Cohort 1 maf file (primary_maf)", "Cohort 2 maf file (relapse_maf)"] [maftools.paramters.readfiles.input.comparsion_input.choices] primary_maf = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(maf)', full.names = TRUE), featch_files(c('maf', 'maf.gz'))$file_path)}" relapse_maf = "!!glue {c(list.files(system.file('extdata', package = 'maftools'), '(maf)', full.names = TRUE), featch_files(c('maf', 'maf.gz'))$file_path)}" [maftools.paramters.readfiles.input.comparsion_input.selected] primary_maf = "@>@system.file('extdata', 'APL_primary.maf.gz', package = 'maftools')@<@" relapse_maf = "@>@system.file('extdata', 'APL_relapse.maf.gz', package = 'maftools')@<@" [maftools.paramters.readfiles.input.other_params] title = "Other paramters" title_control = "class = 'input-section-p'" varname = ["is_tcga"] input_id = ["maftools_is_tcga"] type = ["shiny::checkboxInput"] label = ["Reading file: Maf file is TCGA format? (is_tcga is TRUE)", "Command to read files."] [maftools.paramters.readfiles.input.other_params.value] is_tcga = true [maftools.paramters.readfiles.input.start_analysis] input_id = "start_maftools_analysis" type = "shiny::actionButton" label = "Run" [maftools.paramters.getFields] section_type = "output" rcmd_last = "getFields(laml)" render_type = "shiny::renderPrint" render_id = "maftools_fields_summary" output_type = "shiny::verbatimTextOutput" progressbar_message = "Maftools getFields" [maftools.paramters.getSampleSummary] section_type = "output" rcmd_last = "getSampleSummary(laml)" render_type = "DT::renderDataTable" render_id = "maftools_sample_summary" output_type = "DT::dataTableOutput" progressbar_message = "Maftools getSampleSummary" [maftools.paramters.getGeneSummary] section_type = "output" rcmd_last = "getGeneSummary(laml)" render_type = "DT::renderDataTable" render_id = "maftools_gene_summary" output_type = "DT::dataTableOutput" progressbar_message = "Maftools getGeneSummary" [maftools.paramters.getClinicalData] section_type = "output" render_type = "DT::renderDataTable" render_id = "maftools_clinical_data" output_type = "DT::dataTableOutput" rcmd_last = "getClinicalData(laml)" progressbar_message = "Maftools getClinicalData" [maftools.paramters.plotmafSummary] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_maf_summary" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 14, units='cm', bg='transparent'" rcmd_last = """plotmafSummary(maf = laml, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = FALSE)""" progressbar_message = "Maftools plotmafSummary" [maftools.paramters.oncoplot_default] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_oncoplots" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 14, units='cm', bg='transparent'" rcmd_last = "oncoplot(maf = laml, top = 10, fontSize = 12)" progressbar_message = "Maftools oncoplot_default" [maftools.paramters.oncoplot_with_cnv] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_oncoplots_cnv" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 14, units='cm', bg='transparent'" rcmd_last = "oncoplot(maf = laml.plus.gistic, top = 10, fontSize = 12)" progressbar_message = "Maftools oncoplot with CNV" [maftools.paramters.oncoplot_advanced] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_oncoplots_advanced" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 27, units='cm', bg='transparent'" rcmd_preprocess = """ col = RColorBrewer::brewer.pal(n = 8, name = 'Paired') names(col) = c('Frame_Shift_Del','Missense_Mutation', 'Nonsense_Mutation', 'Multi_Hit', 'Frame_Shift_Ins', 'In_Frame_Ins', 'Splice_Site', 'In_Frame_Del') #Color coding for FAB classification; try getAnnotations(x = laml) to see available annotations. fabcolors = RColorBrewer::brewer.pal(n = 8,name = 'Spectral') names(fabcolors) = c("M0", "M1", "M2", "M3", "M4", "M5", "M6", "M7") fabcolors = list(FAB_classification = fabcolors) mutsigQval = 0.01 clinicalFeatures = "FAB_classification" sortByAnnotation = TRUE oncoplot_advanced_params <- list(maf = laml, colors = col, mutsig = laml_mutsig, mutsigQval = mutsigQval, clinicalFeatures = clinicalFeatures, sortByAnnotation = sortByAnnotation, annotationColor = fabcolors) """ rcmd_last = """ do.call(oncoplot, oncoplot_advanced_params) """ progressbar_message = "Maftools oncoplot with advanced" [maftools.paramters.plotTiTv] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_titv" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_preprocess = "laml.titv = titv(maf = laml, plot = FALSE, useSyn = TRUE)" rcmd_last = "plotTiTv(res = laml.titv)" progressbar_message = "Maftools plotTiTv" [maftools.paramters.lollipopPlot] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_lollipop" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = """lollipopPlot(maf = laml, gene = 'DNMT3A', AACol = 'Protein_Change', showMutationRate = TRUE)""" progressbar_message = "Maftools lollipopPlot" [maftools.paramters.lollipopPlot2] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_lollipop2" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = """lollipopPlot2(m1 = primary_maf, m2 = relapse_maf, gene = "PML", AACol1 = "amino_acid_change", AACol2 = "amino_acid_change", m1_name = "Primary", m2_name = "Relapse")""" progressbar_message = "Maftools lollipopPlot2" [maftools.paramters.tcgaCompare] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_mutation_load" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = "laml.mutload = tcgaCompare(maf = laml, cohortName = 'Example-LAML')" progressbar_message = "Maftools tcgaCompare" [maftools.paramters.plotVaf] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_vaf_box" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = "plotVaf(maf = laml, vafCol = 'i_TumorVAF_WU')" progressbar_message = "Maftools plotVaf" [maftools.paramters.gisticChromPlot] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_gistic_genome" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = """gisticChromPlot(gistic = laml.gistic, markBands = "all")""" progressbar_message = "Maftools gisticChromPlot" [maftools.paramters.gisticBubblePlot] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_gistic_bubble" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = """gisticBubblePlot(gistic = laml.gistic)""" progressbar_message = "Maftools gisticBubblePlot" [maftools.paramters.gisticOncoPlot] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_gistic_oncoplot" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = """gisticOncoPlot(gistic = laml.gistic, clinicalData = getClinicalData(x = laml), clinicalFeatures = 'FAB_classification', sortByAnnotation = TRUE, top = 10)""" progressbar_message = "Maftools gisticOncoPlot" [maftools.paramters.somaticInteractions] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_somatic_inter" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = """somaticInteractions(maf = laml, top = 25, pvalue = c(0.05, 0.1))""" progressbar_message = "Maftools somaticInteractions" [maftools.paramters.oncostrip] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_somatic_inter_oncostrip" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = """oncostrip(maf = laml, genes = c('TP53', 'FLT3', 'RUNX1'))""" progressbar_message = "Maftools oncostrip" [maftools.paramters.plotOncodrive] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_oncodrive" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_preprocess = """laml.sig = oncodrive(maf = laml, AACol = 'Protein_Change', minMut = 5, pvalMethod = 'zscore')""" rcmd_last = """plotOncodrive(res = laml.sig, fdrCutOff = 0.1, useFraction = TRUE)""" progressbar_message = "Maftools plotOncodrive" [maftools.paramters.mafSurvival] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_survival" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_last = """mafSurvival(maf = laml, genes = 'DNMT3A', time = 'days_to_last_followup', Status = 'Overall_Survival_Status', isTCGA = TRUE)""" progressbar_message = "Maftools mafSurvival" [maftools.paramters.plotEnrichmentResults] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_clinical_enrichment" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_preprocess = "fab.ce = clinicalEnrichment(maf = laml, clinicalFeature = 'FAB_classification')" rcmd_last = """plotEnrichmentResults(enrich_res = fab.ce, pVal = 0.05)""" progressbar_message = "Maftools plotEnrichmentResults" [maftools.paramters.plotClusters] section_type = "output" render_type = "shiny::renderPlot" render_id = "maftools_plot_clusters" output_type = "shiny::plotOutput" export_engine = "Cairo" export_params = "type = 'pdf', width = 21, height = 17, units='cm', bg='transparent'" rcmd_preprocess = "tcga.ab.2972.het = inferHeterogeneity(maf = laml, tsb = 'TCGA-AB-2972', vafCol = 'i_TumorVAF_WU')" rcmd_last = "plotClusters(clusters = tcga.ab.2972.het)" progressbar_message = "Maftools maftools_plot_clusters"