MD-Anderson-Bioinformatics/NGCHM-R
Next Generation Clustered Heat Maps

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MD-Anderson-Bioinformatics/NGCHM-R: Next Generation Clustered Heat Maps
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API

API for MD-Anderson-Bioinformatics/NGCHM-R
Next Generation Clustered Heat Maps

Global functions
$.shaidyRepo Man page
+ Man page
+,ngchmVersion2,ngchmAxis-method Man page
.initNGCHM Source code
.onAttach Source code
.onLoad Source code
NGCHM Man page
NGCHM-functions Man page
NGCHM-initialization Man page
NGCHM-package Man page
URLparts Source code
addDefaultCovariate Source code
addDefaultCovariateProperties Source code
addFunDefine Source code
addToolBoxes Source code
appendRendererIfNew Source code
as.dendrogram.shaid Source code
as.hclust.shaid Source code
bindExtraParams Source code
build_container_hierarchy Source code
castAsInteger Man page Source code
castListAsInteger Man page Source code
checkForExternalUtilities Source code
checkForJavaVersion Source code
checkForNGCHMDemoData Source code
checkForNGCHMSupportFilesENVs Source code
checkLabel Source code
checkPropertyValue Source code
chmAdd Man page
chmAdd,ngchm-method Man page
chmAddAutoMenuItems Source code
chmAddAxis Source code
chmAddAxisType Man page
chmAddAxisType,ngchm,character,character,character-method Man page
chmAddAxisType,ngchm,character,character,missing-method Man page
chmAddAxisType,ngchm,character,character,ngchmJS-method Man page
chmAddCSS Man page
chmAddCSS,ngchm,character,character-method Man page
chmAddCSS,ngchm,character-method Man page
chmAddColormap Man page
chmAddColormap,ngchm,ngchmColormap-method Man page
chmAddCovariate Man page
chmAddCovariate,ngchmDataset,character,ngchmCovariate-method Man page
chmAddCovariateBar Man page
chmAddCovariateBar,ngchm,character,list-method Man page
chmAddCovariateBar,ngchm,character,ngchmBar-method Man page
chmAddCovariateBar,ngchm,character,ngchmCovariate-method Man page
chmAddCovariateBar,ngchm,character,ngchmCovariateBar-method Man page
chmAddDataset Man page
chmAddDataset,ngchm,ngchmDataset-method Man page
chmAddDialog Man page
chmAddDialog,ngchm,ngchmDialog-method Man page
chmAddLayer Man page
chmAddLayer,ngchm,matrix-method Man page
chmAddLayer,ngchm,ngchmLayer-method Man page
chmAddList Source code
chmAddMenuItem Man page
chmAddMenuItem,ngchm,character,character,character-method Man page
chmAddMenuItem,ngchm,character,character,ngchmJS-method Man page
chmAddMetaData Man page
chmAddMetaData,ngchm,character,character,character-method Man page
chmAddOverview Man page
chmAddOverview,ngchm,character,numeric,numeric-method Man page
chmAddOverview,ngchm,character,optNumeric,optNumeric-method Man page
chmAddPCA Man page Source code
chmAddProperty Man page
chmAddProperty,ngchm,character,character-method Man page
chmAddReducedDim Man page Source code
chmAddRelated Man page
chmAddRelated,ngchm,character,character,character-method Man page
chmAddRelatedGroup Man page
chmAddRelatedGroup,ngchm,character,character,character,character Man page
chmAddRelatedGroup,ngchm,character,character,character,missing-m Man page
chmAddSpecificAxisTypeFunction Man page
chmAddSpecificAxisTypeFunction,ngchm,character,character,charact Man page Man page
chmAddTSNE Man page Source code
chmAddTag Man page
chmAddTag,ngchm,character,character-method Man page
chmAddTag,ngchm,character-method Man page
chmAddTemplate Man page
chmAddTemplate,ngchm,charOrFunction,character,optList-method Man page
chmAddToolboxR Man page
chmAddToolboxR,ngchm,character,character,character,character-met Man page
chmAddToolboxR2 Man page
chmAddToolboxR2,ngchm,character,character,character-method Man page
chmAddToolboxRC Man page
chmAddToolboxRC,ngchm,character,character,character,character-me Man page
chmAddToolboxRC,ngchm,character,character,character-method Man page
chmAddUMAP Man page Source code
chmAddUWOT Man page Source code
chmAddValueProperty Source code
chmAxis Man page Source code
chmAxisType Man page Source code
chmBindFunction Man page
chmBindFunction,character,character,list-method Man page
chmBindFunction,character,ngchmJS,list-method Man page
chmBrowse Man page Source code
chmColOrder<- Man page
chmColOrder<-,ngchm,optDendrogram-method Man page
chmColorMap Man page Source code
chmColorMap<- Man page
chmColors Man page Source code
chmColors<- Man page
chmCovariate Man page Source code
chmCovariateBar Man page Source code
chmCreateCollection Man page Source code
chmCreateManagedServer Man page Source code
chmCreateServer Man page Source code
chmCurrentCollection Man page Source code
chmCurrentServer Man page Source code
chmDefaultColOrder Man page Source code
chmDefaultRowOrder Man page Source code
chmDeployServer Man page
chmDeployServer,ngchmServer-method Man page
chmExportToFile Man page Source code
chmExportToHTML Man page Source code
chmExportToPDF Man page Source code
chmFieldAccessFunction Man page Source code
chmFixCovariateVersion Source code
chmFixDatasetVersion Source code
chmFixVersion Source code
chmGetDataset Man page
chmGetDataset,ngchmLayer-method Man page
chmGetDeployServerConfig Man page Source code
chmGetFunction Man page Source code
chmGetOverview Man page Source code
chmGetProperty Man page
chmGetProperty,ngchmVersion2,character-method Man page
chmGetProperty,ngchmVersion2-method Man page
chmGetTypeInfo Man page Source code
chmGetURL Man page
chmGetURL,character-method Man page
chmGetURL,ngchm-method Man page
chmHasProperty Man page
chmHasProperty,ngchmVersion2,character-method Man page
chmHasProperty,ngchmVersion2-method Man page
chmInstall Man page
chmInstall,ngchm-method Man page
chmLabel Man page Source code
chmLabel<- Man page
chmLayer Man page Source code
chmLayer<- Man page
chmListFunctions Man page Source code
chmListServers Man page Source code
chmListTypes Man page Source code
chmLoadCHM Man page
chmLoadCHM,character,character-method Man page
chmLoadCHM,character,missing-method Man page
chmLoadCHM,ngchmServer,character-method Man page
chmLoadShaidyCHM Man page
chmMake Man page
chmMake,ngchm-method Man page
chmMakePrivate Man page
chmMakePrivate,character,character-method Man page
chmMakePrivate,character,ngchm-method Man page
chmMakePrivate,ngchmServer,character-method Man page
chmMakePrivate,ngchmServer,ngchm-method Man page
chmMakePublic Man page
chmMakePublic,character,character-method Man page
chmMakePublic,character,ngchm-method Man page
chmMakePublic,ngchmServer,character-method Man page
chmMakePublic,ngchmServer,ngchm-method Man page
chmManager Man page Source code
chmName Man page
chmName,ngchm-method Man page
chmNew Man page Source code
chmNewColorMap Man page Source code
chmNewCovariate Man page Source code
chmNewCovariateBar Man page Source code
chmNewDataLayer Man page Source code
chmNewDataset Man page Source code
chmNewDialog Man page Source code
chmNewFunction Man page Source code
chmNewProperty Man page Source code
chmNewServer Man page Source code
chmOperatorAdd Source code
chmOriginalColOrder Man page Source code
chmOriginalRowOrder Man page Source code
chmProperties Man page Source code
chmProperty Man page Source code
chmProperty<- Man page
chmRandomColOrder Man page Source code
chmRandomRowOrder Man page Source code
chmRegisterAxisFunction Man page Source code
chmRegisterFunction Man page Source code
chmRegisterGetMetadataFunction Man page Source code
chmRegisterMatrixFunction Man page Source code
chmRegisterToolboxFunction Man page Source code
chmRegisterType Man page Source code
chmRegisterTypeMapper Man page Source code
chmRegisterTypeSplitter Man page Source code
chmRowOrder<- Man page
chmRowOrder<-,ngchm,optDendrogram-method Man page
chmServer Man page Source code
chmServerCheck Source code
chmSetCollection Man page Source code
chmSetCredentials Man page
chmSetCredentials,character,character-method Man page
chmSetCredentials,ngchmServer,character-method Man page
chmSetDeployServerConfig Man page Source code
chmSetDisplayLength Man page
chmSetDisplayLength,ngchmVersion2-method Man page
chmStringopFunction Man page Source code
chmTreeGaps Man page Source code
chmUU Source code
chmUninstall Man page
chmUninstall,character-method Man page
chmUninstall,ngchm-method Man page
chmUrlBase Man page
chmUrlBase,ngchmServer-method Man page
chmUserDendrogramToShaid Source code
chmUserLabelsToShaid Source code
chmWriteCustomJS Man page Source code
classstr Source code
container Man page Source code
container-class Man page
cos.dist1 Source code
datestamp Source code
default_panel_configuration Man page Source code
defineMapper Source code
dendfixh Source code
detailMap Man page Source code
detailMap-class Man page
dim.ngchmLayer Source code
dim.ngchmVersion2 Source code
dimnames.ngchmLayer Source code
dimnames.ngchmVersion2 Source code
enforceRange Source code
genSpecFeedback Source code
getAllAxisFunctions Source code
getAllAxisTypeFunctions Source code
getAllAxisTypes Source code
getAllMatrixTypeFunctions Source code
getAxisData Source code
getBuilderJar Source code
getConfigDirs Source code
getDimensions Man page Source code
getDimensions,Seurat Man page
getDimensions,prcomp Man page
getDimensions,umap Man page
getDimensions.Seurat Man page Source code
getDimensions.default Man page Source code
getDimensions.prcomp Man page Source code
getDimensions.umap Man page Source code
getExtraParams Source code
getFnsRqrd Source code
getSeriesProps Source code
getServerVersion Source code
getTypeMatches Source code
getValueExpr Source code
get_all_pane_ids Source code
get_all_panes Source code
getuuid Source code
gitHashObject Man page Source code
gitSha Source code
hasSeries Source code
hasSpecialProperties Source code
initLogging Man page Source code
isany Source code
jsGetOptTag Source code
jsGetTag Source code
jsTagExists Source code
jsonColorMap Source code
listFix Source code
loadChmFromURL Source code
loadConfigDir Source code
loadJavascript Source code
loadNGCHMDemoData Source code
loadNGCHMSupportFiles Source code
loadTextConfig Source code
make.js.names Source code
metaToShaid Source code
namesdifferror Source code
ngchm-class Man page
ngchmAddDatasetBlob Man page Source code
ngchmAddMatrixToCollection Man page Source code
ngchmAddObjectToCollection Man page Source code
ngchmAxis-class Man page
ngchmAxisFunction-class Man page
ngchmAxisType-class Man page
ngchmBar-class Man page
ngchmCSS-class Man page
ngchmCollectionInCollection Man page Source code
ngchmCollectionTree Man page Source code
ngchmColormap-class Man page
ngchmCovariate-class Man page
ngchmCreateServerProtocol Man page Source code
ngchmDataset-class Man page
ngchmDialog-class Man page
ngchmFindRepo Man page Source code
ngchmGetDataFileShaid Man page Source code
ngchmGetEnv Man page Source code
ngchmGetHandleHTTR Man page Source code
ngchmGetLabels Man page Source code
ngchmGetLabelsStr Man page Source code
ngchmGetProtoParam Man page Source code
ngchmGetServerProtocol Man page Source code
ngchmInitShaidyRepository Man page Source code
ngchmJS-class Man page
ngchmLayer-class Man page
ngchmListServerProtocols Man page Source code
ngchmLoadDatasetBlob Man page Source code
ngchmMakeFormat.original Man page Source code
ngchmMakeFormat.shaidy Man page Source code
ngchmMatrixFunction-class Man page
ngchmMenuItem-class Man page
ngchmMetaData-class Man page
ngchmNewBar Man page Source code
ngchmNewCollection Man page Source code
ngchmOverview-class Man page
ngchmProperty-class Man page
ngchmProtoParamCheck Man page Source code
ngchmPushSourceRepository Man page Source code
ngchmPushSourceServer Man page Source code
ngchmPushTempRepository Man page Source code
ngchmRegisterServer Man page Source code
ngchmRelated-class Man page
ngchmRelatedGroup-class Man page
ngchmRenderChm Man page Source code
ngchmResponseJSON Man page Source code
ngchmRowCenter Man page Source code
ngchmSaveAsDatasetBlob Man page Source code
ngchmSaveAsDendrogramBlob Man page Source code
ngchmSaveChmAsBlob Man page Source code
ngchmSaveLabelsAsBlob Source code
ngchmSaveTemplateAsBlob Source code
ngchmServer-class Man page
ngchmServerProtocol-class Man page
ngchmShaidyInit Source code
ngchmTemplate-class Man page
ngchmTileDataset Man page Source code
ngchmTypeMapper-class Man page
ngchmUnregisterServer Man page Source code
ngchmValueProp-class Man page
ngchmVersion2-class Man page
nleaves Source code
nr.as.hclust.dendrogram Source code
nr.str.dendrogram Source code
optDendrogram-class Man page
orderMethod Source code
pane Man page Source code
pane-class Man page
panel_configuration Man page Source code
panel_configuration-class Man page
panel_layout-class Man page
parseJSDoc Source code
parsePathSpec Source code
plot.ngchmVersion2 Man page Source code
pluginPane Man page Source code
pluginPane-class Man page
postBuildFeedback Source code
prepChmOrderings Source code
prepDataLayer Source code
print.ngchm.type.info Man page Source code
print.shaidyRepo Man page Source code
progressFeedback Source code
readConfigFile Source code
readTile Source code
requiredFunctions Source code
s4ToJSON Source code
s4ToList Source code
sameColormap Source code
shaid-class Man page
shaidyAddFileBlob Man page Source code
shaidyBlobExists Man page Source code
shaidyCopyBlob Man page Source code
shaidyCreateProtoBlob Man page Source code
shaidyFinalizeProtoBlob Man page Source code
shaidyFindRepo Man page Source code
shaidyGetComponents Man page
shaidyGetComponents,ngchm-method Man page
shaidyGetComponents,ngchmCovariate-method Man page
shaidyGetComponents,ngchmDataset-method Man page
shaidyGetShaid Man page
shaidyGetShaid,ngchm-method Man page
shaidyHashProtoBlob Man page Source code
shaidyInit Source code
shaidyInitRepository Man page Source code
shaidyLoadProvenanceDB Man page Source code
shaidyLoadProvidDB Man page Source code
shaidyLoadRepository Man page Source code
shaidyNewCache Man page Source code
shaidyProvenance Man page Source code
shaidyRegisterRepoAPI Source code
shaidyRepoAPI Man page Source code
shortnameslist Source code
spstrip Source code
summaryMap Man page Source code
summaryMap-class Man page
systemCheck Source code
testJava Source code
treeCuts-class Man page
utempfile Source code
validateAxisOrder Source code
validateColor Source code
validateCovariateBar Source code
validateNewAxisOrder Source code
validateNewCovariateBar Source code
validateNewLayer Source code
validate_child_panes Source code
validate_sizes Source code
verifyNumeric Man page Source code
writeBinLines Source code
writeCSS Source code
writeChm Source code
writeChmExtraSupport Source code
writeChmPost Source code
writeColorMap Source code
writeCovariateBar Source code
writeCustomJS Source code
writeDataLayer Source code
writeDataset Source code
writeDialogs Source code
writeHCDataTSVs Source code
writeJS Source code
writeMenu Source code
writeMeta Source code
writeOrder Source code
writeProperties Source code
writePropertiesPost Source code
writeRelated Source code
writeRelatedGroup Source code
writeTemplate Source code
writeTile Source code
MD-Anderson-Bioinformatics/NGCHM-R documentation built on June 9, 2025, 8:04 p.m.

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