ImmuneSpaceConnection: The ImmuneSpaceConnection class
In ImmuneSpaceR: A Thin Wrapper around the ImmuneSpace Database
Description
Details
Value
Constructor
Fields
Methods
Methods
See Also
Examples
Description
A connection respresents a study or a set of studies available on ImmuneSpace.
It provides function to download and display the data within these studies.
Details
The ImmuneSpaceConnection will initialize itself, and look for a
.netrc file in "~/" the user's home directory. The
.netrc file should contain a machine, login, and
password entry to allow access to ImmuneSpace, where machine is
the host name like "www.immunespace.org".
It can also use global variables labkey.url.base, and
labkey.url.path, to access a study. labkey.url.base should be
https://www.immunespace.org/. labkey.url.path should be
/Studies/studyname, where 'studyname' is the accession number of the
study.
Value
An instance of an ImmuneSpaceConnection for a study in
labkey.url.path.
Constructor
CreateConnection
Fields
study-
A character. The study accession number. Use an empty string ("")
to create a connection at the project level.
availableDatasets-
A data.table. The table of datasets available in the connection
object.
cache-
A list. Stores the data to avoid downloading the same tables
multiple times.
config-
A list. Stores configuration of the connection object such as
URL, path and username.
Methods
initialize()-
Initialize ImmuneSpaceConnection class.
See CreateConnection.
print()-
Print ImmuneSpaceConnection class.
listDatasets(output = c("datasets", "expression"))-
Lists the datasets available in the study or studies of the connection.
listGEMatrices(verbose = FALSE, reload = FALSE, participantIds = NULL)-
Lists available gene expression matrices for the connection.
verbose: A logical. If TRUE, whether to print the extra details
for troubleshooting.
reload: A logical. If TRUE, retrieve the table of available gene
expression matrices whether a cached version exist or not.
participantIds: A character vector of participant ids to filter
by. Only matrices with data from participantIds will be returned.
If NULL, all matrices are returned.
listGEAnalysis()-
Lists available gene expression analysis for the connection.
listParticipantGroups()-
Lists available participant groups on the ImmuneSpace portal.
listParticipantGEMatrices(group, verbose = FALSE)-
Lists available gene expression matrices for participants in group.
group: A character or integer.
Call con$listParticipantGroups() to see available participants
groups. Use group_id or group_name as input.
verbose: A logical. If TRUE, whether to print the extra details
for troubleshooting.
listWorkspaces(reload = FALSE)-
Lists available workspaces for the connection.
reload: A logical. If TRUE, download the table whether a cached
version exist or not.
listGatingSets(reload = FALSE)-
Lists available gating sets for the connection.
reload: A logical. If TRUE, download the table whether a cached
version exist or not.
summarizeCyto()-
Prints a summary of cytometry data for the connection.
summarizeGatingSet(gatingSet)-
Prints a summary of a gating set. Note that this method currently works
only in the ImmuneSpace RStudio session.
gatingSet: A character. The name of the gating set to summarize.
loadGatingSet(gatingSet)-
Loads a gating set via flowWorkspace::load_gs to the
current environment. Note that this method currently works only in the
ImmuneSpace RStudio Docker session.
gatingSet: A character. The name of the gating set to load.
getDataset(x, original_view = FALSE, reload = FALSE,
colFilter = NULL, ...)-
Get a dataset form the connection.
x: A character. The name of the dataset to download.
original_view: A logical. If TRUE, download the original ImmPort
view; else, download the default grid view.
reload: A logical. If TRUE, download the dataset whether a cached
version exist or not.
colFilter: A character. A filter as returned by Rlabkey's
makeFilter function.
...: Extra arguments to be passed to labkey.selectRows.
getGEMatrix(matrixName = NULL, cohortType = NULL,
outputType = "summary", annotation = "latest", reload = FALSE,
verbose = FALSE)-
Downloads a probe-level or gene-symbol summarized expression matrix from
ImmuneSpace and constructs an ExpressionSet. Use experimentData()
on the resulting ExpressionSet object to see version info for annotation.
matrixName: A character. The name of the gene expression matrix
to download.
cohortType: A character. The name of a cohortType that has an
associated gene expression matrix. Note that if this argument is not
NULL, then matrixName is ignored. CohortType is a concatenation of
"cohort" and "cell type" that allows the user to specify a matrix for the
cell type subset of a cohort.
outputType: A character. one of 'raw', 'normalized' or 'summary'.
If 'raw', returns an expression matrix of non-normalized values by probe.
'normalized' returns normalized values by probe. 'summary' returns
normalized values averaged by gene symbol.
annotation: A character. one of 'default', 'latest', or 'ImmSig'.
Determines which feature annotation set (FAS) is used. 'default' uses the
FAS from when the matrix was generated. latest' uses a recently updated
FAS based on the original. 'ImmSig' is specific to studies involved in
the ImmuneSignatures project and uses the annotation from when the
meta-study's manuscript was created.
reload: A logical. If set to TRUE, the matrix will be downloaded
again, even if a cached copy exists in the ImmuneSpaceConnection object.
verbose: A logical. If set to TRUE, notes on how the expressionSet
object was created will be printed, including normalization, summarization,
feature_annotation_set, and alias2symbol mapping version of org.Hs.eg.db.
getGEAnalysis(...)-
Downloads data from the gene expression analysis results table.
...: A list of arguments to be passed to labkey.selectRows.
getGEInputs()-
Downloads data from the gene expression input samples table.
getParticipantData(group, dataType, original_view = FALSE,
...)-
Returns a data.table with data subset by participant group.
group: A character or integer.
Call con$listParticipantGroups() to see available participants
groups. Use group_id or group_name as input.
dataType: A character. Use con$availableDatasets to see
available dataset names.
getParticipantGEMatrix(group, outputType = "summary",
annotation = "latest", reload = FALSE)-
Downloads probe-level or gene-symbol summarized expression matrices for all
participants within group from ImmuneSpace and constructs an
ExpressionSet containing observations for each participant in group
where gene expression data is available.
group: A character or integer.
Call con$listParticipantGroups() to see available participants
groups. Use group_id or group_name as input.
outputType: A character. one of 'raw', 'normalized' or 'summary'.
If 'raw', returns an expression matrix of non-normalized values by probe.
'normalized' returns normalized values by probe. 'summary' returns
normalized values averaged by gene symbol.
annotation: A character. one of 'default', 'latest', or 'ImmSig'.
Determines which feature annotation set (FAS) is used. 'default' uses the
FAS from when the matrix was generated. latest' uses a recently updated
FAS based on the original. 'ImmSig' is specific to studies involved in
the ImmuneSignatures project and uses the annotation from when the
meta-study's manuscript was created.
reload: A logical. If set to TRUE, matrices will be downloaded
again, even if a cached copy exists in the ImmuneSpaceConnection object.
downloadGEFiles(files, destdir = ".")-
Downloads gene expression raw data files.
files: A character. Filenames as shown on the
gene_expression_files dataset.
destdir: A character. The local path to store the downloaded
files.
addTreatment(expressionSet)-
Adds treatment information to the phenoData of an ExpressionSet.
expressionSet: An ExpressionSet. The ExpressionSet object that has
been downloaded from the connection.
mapSampleNames(EM = NULL, colType = "participant_id")-
Changes the sampleNames of an ExpressionSet fetched by getGEMatrix
using the information in the phenodData slot.
EM: An ExpressionSet, as returned by getGEMatrix.
colType: A character. The type of column names. Valid options are
'expsample_accession' and 'participant_id'.
plot(...)-
Visualizes a selected dataset. This method is used by the DataExplorer
module on the ImmuneSpace portal.
dataset: A character. The name of the dataset to plot, as
displayed by the listDataset method.
normalize_to_baseline: A logical. If TRUE, the values are plotted
as log2 fold-change from baseline.
type: A character. The type of plot. Valid choices are 'auto',
'heatmap', 'boxplot', 'lineplot', 'violinplot'. If set to 'auto', the
function will select an appropriate plot type for the selected data.
filter: A filter as created by the makeFilter function from
Rlabkey.
facet: The facetting for ggplot2 based plots. Valid choices are
'grid' and 'wrap'.
text_size: The size of all text elements in the plot.
legend: A character. Columns of the dataset or demographics to be
added as legend on the heatmap. This argument is ignored if the plot type
isn't heatmap.
show_virus_strain: A logical. Should all the virus strains be
shown or should the values be averaged. Only used when dataset = 'hai'.
interactive: A logical. If TRUE, an interactive plot will be
created. The default is FALSE.
...: Extra argument to be passed to ggplot. e.g: shape = 'Age',
color = 'Race'.
clearCache()-
Clears the cache. Removes downloaded datasets and expression matrices.
Methods
Public methods
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Method listWorkspaces()
Usage
ISCon$listWorkspaces(reload = FALSE)
Method listGatingSets()
Usage
ISCon$listGatingSets(reload = FALSE)
Method summarizeCyto()
Usage
ISCon$summarizeCyto()
Method summarizeGatingSet()
Usage
ISCon$summarizeGatingSet(gatingSet)
Method loadGatingSet()
Usage
ISCon$loadGatingSet(gatingSet)
Method listDatasets()
Usage
ISCon$listDatasets(output = c("datasets", "expression"))
Method getDataset()
Usage
ISCon$getDataset(
x,
original_view = FALSE,
reload = FALSE,
colFilter = NULL,
transformMethod = "none",
...
)
Method listGEMatrices()
Usage
ISCon$listGEMatrices(verbose = FALSE, reload = FALSE, participantIds = NULL)
Method listGEAnalysis()
Usage
ISCon$listGEAnalysis()
Method getGEMatrix()
Usage
ISCon$getGEMatrix(
matrixName = NULL,
cohortType = NULL,
outputType = "summary",
annotation = "latest",
reload = FALSE,
verbose = FALSE
)
Method getGEAnalysis()
Usage
ISCon$getGEAnalysis(...)
Method getGEInputs()
Usage
ISCon$getGEInputs()
Method getGEFiles()
Usage
ISCon$getGEFiles(files, destdir = ".", quiet = FALSE)
Method downloadGEFiles()
Usage
ISCon$downloadGEFiles(files, destdir = ".")
Method addTreatment()
Usage
ISCon$addTreatment(expressionSet)
Method mapSampleNames()
Usage
ISCon$mapSampleNames(EM = NULL, colType = "participant_id")
Method listParticipantGroups()
Usage
ISCon$listParticipantGroups()
Method getParticipantData()
Usage
ISCon$getParticipantData(
group,
dataType,
original_view = FALSE,
reload = FALSE,
colFilter = NULL,
transformMethod = "none",
...
)
Method listParticipantGEMatrices()
Usage
ISCon$listParticipantGEMatrices(group, verbose = FALSE)
Method getParticipantGEMatrix()
Usage
ISCon$getParticipantGEMatrix(
group,
outputType = "summary",
annotation = "latest",
reload = FALSE
)
Method plot()
Usage
ISCon$plot(...)
Method print()
Usage
ISCon$print()
Method clearCache()
Usage
ISCon$clearCache()
Method new()
Usage
ISCon$new(
study = NULL,
login = NULL,
password = NULL,
verbose = FALSE,
onTest = FALSE
)
Method clone()
The objects of this class are cloneable with this method.
Usage
ISCon$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
CreateConnection ImmuneSpaceR-package
Examples
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## Not run:
# Create a connection (Initiate a ImmuneSpaceConnection object)
sdy269 <- CreateConnection("SDY269")
# Print the connection object
sdy269
# Retrieve the HAI dataset
HAI <- sdy269$getDataset("hai")
# Fetch a summarized gene expresssion matrix with latest annotation
LAIV <- sdy269$getGEMatrix("LAIV_2008")
# Visualize the ELISA dataset
sdy269$plot("elisa")
## End(Not run)
sdy <- try(CreateConnection("SDY269"))
if (inherits(sdy, "try-error")) {
warning("Read the Introduction vignette for more information on how to set
up a .netrc file.")
}
ImmuneSpaceR documentation built on Dec. 21, 2020, 2:01 a.m.
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Description Details Value Constructor Fields Methods Methods See Also Examples
Description
A connection respresents a study or a set of studies available on ImmuneSpace. It provides function to download and display the data within these studies.
Details
The ImmuneSpaceConnection will initialize itself, and look for a
.netrc file in "~/" the user's home directory. The
.netrc file should contain a machine, login, and
password entry to allow access to ImmuneSpace, where machine is
the host name like "www.immunespace.org".
It can also use global variables labkey.url.base, and
labkey.url.path, to access a study. labkey.url.base should be
https://www.immunespace.org/. labkey.url.path should be
/Studies/studyname, where 'studyname' is the accession number of the
study.
Value
An instance of an ImmuneSpaceConnection for a study in
labkey.url.path.
Constructor
CreateConnection
Fields
study-
A
character. The study accession number. Use an empty string ("") to create a connection at the project level. availableDatasets-
A
data.table. The table of datasets available in the connection object. cache-
A
list. Stores the data to avoid downloading the same tables multiple times. config-
A
list. Stores configuration of the connection object such as URL, path and username.
Methods
initialize()-
Initialize
ImmuneSpaceConnectionclass. SeeCreateConnection. print()-
Print
ImmuneSpaceConnectionclass. listDatasets(output = c("datasets", "expression"))-
Lists the datasets available in the study or studies of the connection.
listGEMatrices(verbose = FALSE, reload = FALSE, participantIds = NULL)-
Lists available gene expression matrices for the connection.
verbose: A logical. If TRUE, whether to print the extra details for troubleshooting.reload: A logical. If TRUE, retrieve the table of available gene expression matrices whether a cached version exist or not.participantIds: A character vector of participant ids to filter by. Only matrices with data fromparticipantIdswill be returned. IfNULL, all matrices are returned. listGEAnalysis()-
Lists available gene expression analysis for the connection.
listParticipantGroups()-
Lists available participant groups on the ImmuneSpace portal.
listParticipantGEMatrices(group, verbose = FALSE)-
Lists available gene expression matrices for participants in
group.group: A character or integer. Callcon$listParticipantGroups()to see available participants groups. Use group_id or group_name as input.verbose: A logical. If TRUE, whether to print the extra details for troubleshooting. listWorkspaces(reload = FALSE)-
Lists available workspaces for the connection.
reload: A logical. If TRUE, download the table whether a cached version exist or not. listGatingSets(reload = FALSE)-
Lists available gating sets for the connection.
reload: A logical. If TRUE, download the table whether a cached version exist or not. summarizeCyto()-
Prints a summary of cytometry data for the connection.
summarizeGatingSet(gatingSet)-
Prints a summary of a gating set. Note that this method currently works only in the ImmuneSpace RStudio session.
gatingSet: A character. The name of the gating set to summarize. loadGatingSet(gatingSet)-
Loads a gating set via
flowWorkspace::load_gsto the current environment. Note that this method currently works only in the ImmuneSpace RStudio Docker session.gatingSet: A character. The name of the gating set to load. getDataset(x, original_view = FALSE, reload = FALSE, colFilter = NULL, ...)-
Get a dataset form the connection.
x: A character. The name of the dataset to download.original_view: A logical. If TRUE, download the original ImmPort view; else, download the default grid view.reload: A logical. If TRUE, download the dataset whether a cached version exist or not.colFilter: A character. A filter as returned by Rlabkey'smakeFilterfunction....: Extra arguments to be passed tolabkey.selectRows. getGEMatrix(matrixName = NULL, cohortType = NULL, outputType = "summary", annotation = "latest", reload = FALSE, verbose = FALSE)-
Downloads a probe-level or gene-symbol summarized expression matrix from ImmuneSpace and constructs an ExpressionSet. Use
experimentData()on the resulting ExpressionSet object to see version info for annotation.matrixName: A character. The name of the gene expression matrix to download.cohortType: A character. The name of a cohortType that has an associated gene expression matrix. Note that if this argument is not NULL, thenmatrixNameis ignored. CohortType is a concatenation of "cohort" and "cell type" that allows the user to specify a matrix for the cell type subset of a cohort.outputType: A character. one of 'raw', 'normalized' or 'summary'. If 'raw', returns an expression matrix of non-normalized values by probe. 'normalized' returns normalized values by probe. 'summary' returns normalized values averaged by gene symbol.annotation: A character. one of 'default', 'latest', or 'ImmSig'. Determines which feature annotation set (FAS) is used. 'default' uses the FAS from when the matrix was generated. latest' uses a recently updated FAS based on the original. 'ImmSig' is specific to studies involved in the ImmuneSignatures project and uses the annotation from when the meta-study's manuscript was created.reload: A logical. If set to TRUE, the matrix will be downloaded again, even if a cached copy exists in the ImmuneSpaceConnection object.verbose: A logical. If set to TRUE, notes on how the expressionSet object was created will be printed, including normalization, summarization, feature_annotation_set, and alias2symbol mapping version of org.Hs.eg.db. getGEAnalysis(...)-
Downloads data from the gene expression analysis results table.
...: A list of arguments to be passed tolabkey.selectRows. getGEInputs()-
Downloads data from the gene expression input samples table.
getParticipantData(group, dataType, original_view = FALSE, ...)-
Returns a data.table with data subset by participant group.
group: A character or integer. Callcon$listParticipantGroups()to see available participants groups. Use group_id or group_name as input.dataType: A character. Usecon$availableDatasetsto see available dataset names. getParticipantGEMatrix(group, outputType = "summary", annotation = "latest", reload = FALSE)-
Downloads probe-level or gene-symbol summarized expression matrices for all participants within
groupfrom ImmuneSpace and constructs an ExpressionSet containing observations for each participant ingroupwhere gene expression data is available.group: A character or integer. Callcon$listParticipantGroups()to see available participants groups. Use group_id or group_name as input.outputType: A character. one of 'raw', 'normalized' or 'summary'. If 'raw', returns an expression matrix of non-normalized values by probe. 'normalized' returns normalized values by probe. 'summary' returns normalized values averaged by gene symbol.annotation: A character. one of 'default', 'latest', or 'ImmSig'. Determines which feature annotation set (FAS) is used. 'default' uses the FAS from when the matrix was generated. latest' uses a recently updated FAS based on the original. 'ImmSig' is specific to studies involved in the ImmuneSignatures project and uses the annotation from when the meta-study's manuscript was created.reload: A logical. If set to TRUE, matrices will be downloaded again, even if a cached copy exists in the ImmuneSpaceConnection object. downloadGEFiles(files, destdir = ".")-
Downloads gene expression raw data files.
files: A character. Filenames as shown on the gene_expression_files dataset.destdir: A character. The local path to store the downloaded files. addTreatment(expressionSet)-
Adds treatment information to the phenoData of an ExpressionSet.
expressionSet: An ExpressionSet. The ExpressionSet object that has been downloaded from the connection. mapSampleNames(EM = NULL, colType = "participant_id")-
Changes the sampleNames of an ExpressionSet fetched by
getGEMatrixusing the information in the phenodData slot.EM: An ExpressionSet, as returned bygetGEMatrix.colType: A character. The type of column names. Valid options are 'expsample_accession' and 'participant_id'. plot(...)-
Visualizes a selected dataset. This method is used by the DataExplorer module on the ImmuneSpace portal.
dataset: A character. The name of the dataset to plot, as displayed by the listDataset method.normalize_to_baseline: A logical. If TRUE, the values are plotted as log2 fold-change from baseline.type: A character. The type of plot. Valid choices are 'auto', 'heatmap', 'boxplot', 'lineplot', 'violinplot'. If set to 'auto', the function will select an appropriate plot type for the selected data.filter: A filter as created by the makeFilter function from Rlabkey.facet: The facetting for ggplot2 based plots. Valid choices are 'grid' and 'wrap'.text_size: The size of all text elements in the plot.legend: A character. Columns of the dataset or demographics to be added as legend on the heatmap. This argument is ignored if the plot type isn't heatmap.show_virus_strain: A logical. Should all the virus strains be shown or should the values be averaged. Only used when dataset = 'hai'.interactive: A logical. If TRUE, an interactive plot will be created. The default is FALSE....: Extra argument to be passed to ggplot. e.g: shape = 'Age', color = 'Race'. clearCache()-
Clears the cache. Removes downloaded datasets and expression matrices.
Methods
Public methods
Method listWorkspaces()
Usage
ISCon$listWorkspaces(reload = FALSE)
Method listGatingSets()
Usage
ISCon$listGatingSets(reload = FALSE)
Method summarizeCyto()
Usage
ISCon$summarizeCyto()
Method summarizeGatingSet()
Usage
ISCon$summarizeGatingSet(gatingSet)
Method loadGatingSet()
Usage
ISCon$loadGatingSet(gatingSet)
Method listDatasets()
Usage
ISCon$listDatasets(output = c("datasets", "expression"))Method getDataset()
Usage
ISCon$getDataset( x, original_view = FALSE, reload = FALSE, colFilter = NULL, transformMethod = "none", ... )
Method listGEMatrices()
Usage
ISCon$listGEMatrices(verbose = FALSE, reload = FALSE, participantIds = NULL)
Method listGEAnalysis()
Usage
ISCon$listGEAnalysis()
Method getGEMatrix()
Usage
ISCon$getGEMatrix( matrixName = NULL, cohortType = NULL, outputType = "summary", annotation = "latest", reload = FALSE, verbose = FALSE )
Method getGEAnalysis()
Usage
ISCon$getGEAnalysis(...)
Method getGEInputs()
Usage
ISCon$getGEInputs()
Method getGEFiles()
Usage
ISCon$getGEFiles(files, destdir = ".", quiet = FALSE)
Method downloadGEFiles()
Usage
ISCon$downloadGEFiles(files, destdir = ".")
Method addTreatment()
Usage
ISCon$addTreatment(expressionSet)
Method mapSampleNames()
Usage
ISCon$mapSampleNames(EM = NULL, colType = "participant_id")
Method listParticipantGroups()
Usage
ISCon$listParticipantGroups()
Method getParticipantData()
Usage
ISCon$getParticipantData( group, dataType, original_view = FALSE, reload = FALSE, colFilter = NULL, transformMethod = "none", ... )
Method listParticipantGEMatrices()
Usage
ISCon$listParticipantGEMatrices(group, verbose = FALSE)
Method getParticipantGEMatrix()
Usage
ISCon$getParticipantGEMatrix( group, outputType = "summary", annotation = "latest", reload = FALSE )
Method plot()
Usage
ISCon$plot(...)
Method print()
Usage
ISCon$print()
Method clearCache()
Usage
ISCon$clearCache()
Method new()
Usage
ISCon$new( study = NULL, login = NULL, password = NULL, verbose = FALSE, onTest = FALSE )
Method clone()
The objects of this class are cloneable with this method.
Usage
ISCon$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
See Also
CreateConnection ImmuneSpaceR-package
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 | ## Not run:
# Create a connection (Initiate a ImmuneSpaceConnection object)
sdy269 <- CreateConnection("SDY269")
# Print the connection object
sdy269
# Retrieve the HAI dataset
HAI <- sdy269$getDataset("hai")
# Fetch a summarized gene expresssion matrix with latest annotation
LAIV <- sdy269$getGEMatrix("LAIV_2008")
# Visualize the ELISA dataset
sdy269$plot("elisa")
## End(Not run)
sdy <- try(CreateConnection("SDY269"))
if (inherits(sdy, "try-error")) {
warning("Read the Introduction vignette for more information on how to set
up a .netrc file.")
}
|
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