bmbroom/ngchmr

An R library for creating Next-Generation Clustered Heat Maps (NG-CHM)

ngchmr's Issues

Expand Data Layer Functionality

Add functionality for:
Option to display/not display grid lines
Grid line color
Selection color

Classes to Remove and/or Class Documentation Not To Be Exported

Classes to Remove and/or Class Documentation Not To Be Exported
ngchm-class
ngchmColorpt-class
ngchmCSS-class
ngchmDialog-class
ngchmMatrixFunction-class
ngchmRelated-class
ngchmRelatedGroup-class

How is ReadOnly Status To Be Handled in V2 Heatmaps?

Would the user add a readonly item to the metadata properties to make the NGCHM read only?

Expand Server API Functionality

Add function and appropriate documentation for chmAddUnregisterServer(chm) function

Default color scheme for datalayer contains black and missing color also black.

Review Overview API Functionality

For the PDF or other output formats option, do you plan for it to end up working like the PDF function of the viewer does now?
i.e. Should it have options for showing/not showing each dendrograms, will it show covariates, Will trimming of labels be supported?

Complete changes to support version 2 NGCHMs for following functions

Complete changes to support version 2 NGCHMs for following functions
chmAddOverview
chmGetOverview
ngchmTileDataset
chmFieldAccessFunction

Functions To Remove from Export and/or Function Documentation Should Not Be Exported

Methods To Remove from Export and/or Method Documentation Should Not Be Exported

chmAddCSS
chmAddDialog
chmAddRelated
chmAddRelatedGroup
chmAddSpecificAxisTypeFunction
chmAddTag
chmBindFunction
chmGetFunction
chmMake
chmMakePrivate
chmMakePublic
chmNewDialog
chmNewFunction
chmRegisterAxisFunction
chmRegisterFunction
chmRegisterGetMetadataFunction
chmRegisterMatrixFunction
chmRegisterToolboxFunction
chmRegisterTypeMapper
chmRegisterTypeSplitter
chmWriteCustomJS
NGCHM-functions

Using default colors for covariate bars, no "missing value" color is provided by default. The code provides a warning to this effect.

PDF Help file missing documentation for some methods

Missing documentation for:
chmAddList
chmAddAxis

Review Requirements And Make Appropriate Changes To Support Statistics Toolbox In V2 NGCHMS.

Review Requirements And Make Appropriate Changes To Support Statistics Toolbox In V2 NGCHMS.

Expand Covariate Functionality

Add support for
Alternate formats than color bar (scatterplot, histogram, etc.) and related color settings

Improve Support for Label Truncation Options

Rename ngchmVersion2 object member "rowDisplayAbbreviation" to "labelTruncationPoint" or something similar that better explains what it is.

Add methods for setting the values for :
columnDisplayLength (max characters displayed in column label)
columnDisplayAbbreviation (which position to substitute ... in label if too long: Beginning, Middle, End)
rowDisplayLength (max characters in row label)
rowDisplayAbbreviation (which position to substitute ... in label if too long: Beginning, Middle, End)

Expand Dendrogram Functionality

New functionality to add:
Setting dendrogram display height.

Check If Function chmStringopFunction Is Still Needed

Check If Function chmStringopFunction Is Still Needed

Add Support For Row And Column Cuts

Create functions and appropriate documentation for:
chmAddRowCuts
chmAddColumnCuts
chmRemoveRowCuts
chmRemoveColumnCuts

With support for
colCutLocations
colCutWidth
colTreeCuts

Miscellaneous Documentation Issues

chmAddCovariateBar : for the merge argument, it says “default”, but doesn’t list what the default is.
chmGetUrl : The item “server” is duplicated in the RD file. This seems to be ignored when making the PDF, but is displayed twice when asking for help within R.

Functions Where Function Documentation Should Not Be Exported

Methods Where Method Documentation Should Not Be Exported

ngchmAddDatasetBlob
ngchmAddMatrixToCollection
ngchmAddObjectToCollection
ngchmCollectionInCollection
ngchmCollectionTree
ngchmCreateServerProtocol
ngchmFindRepo
ngchmGetDataFileShaid
ngchmGetEnv
ngchmGetHandleHTTR
ngchmGetLabels
ngchmGetLabelsStr
ngchmGetProtoParam
ngchmGetServerProtocol
ngchmInitShaidyRepository
ngchmListServerProtocols
ngchmLoadDatasetBlob
ngchmMakeFormat.original
ngchmMakeFormat.shaidy
ngchmNewBar
ngchmNewCollection
ngchmProtoParamCheck
ngchmPushSourceRepository
ngchmPushTempRepository
ngchmRegisterServer
ngchmRenderChm
ngchmResponseJSON
ngchmRowCenter
ngchmSaveAsDatasetBlob
ngchmSaveAsDendrogramBlob
ngchmSaveChmAsBlob
ngchmShaidyInit
ngchmTileDataset
ngchmUnregisterServer
plot.ngchmVersion2
print.ngchm.type.info
print.shaidyRepo
readTile
shaidyAddFileBlob
shaidyBlobExists
shaidyCopyBlob
shaidyCreateProtoBlob
shaidyFinalizeProtoBlob
shaidyFindRepo
shaidyGetComponents
shaidyGetShaid
shaidyHashProtoBlob
shaidyInit
shaidyInitRepository
shaidyLoadProvenanceDB
shaidyLoadProvidDB
shaidyLoadRepository
shaidyNewCache
shaidyProvenance
shaidyRegisterRepoAPI
shaidyRepoAPI
validateNewLayer
writeTile
$.shaidyRepo
cos.dist1
gitHashObject

Remove Following Class Slots From ngchmVersion2 Class

dialogs
tags
rowTypeFunctions
colTypeFunctions
elementTypeFunctions
javascript
relatedLinks
relatedGroups