> ## QC plots
> girafe( ggobj = autoplot( demoData , "lane-bindingDensity" ) )
Error:
! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
! Aesthetics must be either length 1 or the same as the data (75)
x Fix the following mappings: `hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData , "lane-fov" ) )
Error:
! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
! Aesthetics must be either length 1 or the same as the data (75)
x Fix the following mappings: `hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData, "housekeep-geom" ) )
Error:
! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
! Aesthetics must be either length 1 or the same as the data (75)
x Fix the following mappings: `hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData , "ercc-linearity" ) )
Error:
! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
! Aesthetics must be either length 1 or the same as the data (375)
x Fix the following mappings: `hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData , "ercc-lod" ) )
Error:
! Problem while setting up geom aesthetics.
ℹ Error occurred in the 2nd layer.
Caused by error in `cli::cli_abort()`:
! Aesthetics must be either length 1 or the same as the data (75)
x Fix the following mappings: `hover_nearest`, `outlier.data_id`, `outlier.tooltip`, `outlier.onclick`,
`outlier.hover_css`, `outlier.selected_css`, `outlier.tooltip_fill`, and `outlier.hover_nearest`
Run `rlang::last_error()` to see where the error occurred.
> girafe( ggobj = autoplot( demoData , "boxplot-feature" , index = featureNames(demoData)[3] , elt = "exprs" ) )
Error in `stat_boxplot()`:
! Problem while setting up geom aesthetics.
ℹ Error occurred in the 1st layer.
Caused by error in `cli::cli_abort()`:
! Aesthetics must be either length 1 or the same as the data (1)
x Fix the following mappings: `width`
Run `rlang::last_error()` to see where the error occurred.
> demoData <- normalize( demoData , type="nSolver", fromELT = "exprs" , toELT = "exprs_norm" )
Error in normalize(demoData, type = "nSolver", fromELT = "exprs", toELT = "exprs_norm") :
unused arguments (type = "nSolver", fromELT = "exprs", toELT = "exprs_norm")
> autoplot( demoData , "heatmap-genes" , elt = "exprs_norm" )
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 't': 'elt' not present in assayData(object)
>
> demoData
NanoStringRccSet (storageMode: lockedEnvironment)
assayData: 784 features, 75 samples
element names: exprs
protocolData
sampleNames: _01_04.RCC _01_05.RCC ...
(75 total)
varLabels: FileVersion SoftwareVersion ... Sample ID (18 total)
varMetadata: labelDescription
phenoData
sampleNames: _01_04.RCC _01_05.RCC ...
(75 total)
varLabels: Group
varMetadata: labelDescription
featureData
featureNames: Endogenous_CCNO_NM_021147.4 Endogenous_MYC_NM_002467.3 ... Housekeeping_ERCC3_NM_000122.1 (784
total)
fvarLabels: CodeClass GeneName ... BarcodeComments (10 total)
fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation: NS_IO_360_v1.0
signature: none
>
Hi
After reading RCC and annotation file I get this error
Thanks for any help