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Merged
asizemore merged 7 commits into from
Feb 14, 2025
Merged

Have scatter return point ids #264

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c7728db
plain scatterplot returns point IDs when asked
asizemore Feb 6, 2025
675cbbe
fix test
asizemore Feb 7, 2025
1842412
add returnPointIds to scattergl
asizemore Feb 7, 2025
63117b0
fix complete cases table
asizemore Feb 12, 2025
d4b91d0
removed unused failing tests
asizemore Feb 12, 2025
3c21414
fix when returnPointIds is false
asizemore Feb 12, 2025
50e4969
scatter should err if improper idColumn supplied
asizemore Feb 13, 2025
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42 changes: 39 additions & 3 deletions R/class-plotdata-scatter.R
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,8 @@ newScatterPD <- function(.dt = data.table::data.table(),
value = character(),
useGradientColorscale = FALSE,
overlayValues = veupathUtils::BinList(),
idColumn = character(),
returnPointIds = logical(),
correlationMethod = character(),
sampleSizes = logical(),
completeCases = logical(),
Expand All @@ -15,6 +17,8 @@ newScatterPD <- function(.dt = data.table::data.table(),
variables = variables,
useGradientColorscale = useGradientColorscale,
overlayValues = overlayValues,
idColumn = idColumn,
returnPointIds = returnPointIds,
sampleSizes = sampleSizes,
completeCases = completeCases,
evilMode = evilMode,
Expand All @@ -31,6 +35,16 @@ newScatterPD <- function(.dt = data.table::data.table(),
group <- veupathUtils::findColNamesFromPlotRef(variables, 'overlay')
panel <- findPanelColName(veupathUtils::findVariableSpecFromPlotRef(variables, 'facet1'),
veupathUtils::findVariableSpecFromPlotRef(variables, 'facet2'))
# If we ask for the point ids, ensure the column is present. Otherwise set to null.
if (returnPointIds) {
if (!is.null(idColumn) && idColumn %in% names(.dt)) {
idCol <- idColumn
} else {
stop("idColumn not found or not supplied. Supply proper idColumn if returnPointIds is TRUE.")
}
} else {
idCol <- NULL
}

dtForCorr <- data.table::as.data.table(.pd)

Expand All @@ -40,7 +54,7 @@ newScatterPD <- function(.dt = data.table::data.table(),
series <- collapseByGroup(.pd, group = 'overlayMissingData', panel)
.pd$overlayMissingData <- NULL
series$overlayMissingData <- NULL
data.table::setnames(series, c(panel, 'seriesX', 'seriesY', 'seriesGradientColorscale'))
data.table::setnames(series, c(panel, 'seriesX', 'seriesY', 'seriesGradientColorscale', idCol))

# corr results w gradient, same as w/o groups so set group to NULL
dtForCorr[[group]] <- NULL
Expand All @@ -50,7 +64,7 @@ newScatterPD <- function(.dt = data.table::data.table(),
} else {
#series data w/o gradient
series <- collapseByGroup(.pd, group, panel)
data.table::setnames(series, c(group, panel, 'seriesX', 'seriesY'))
data.table::setnames(series, c(group, panel, 'seriesX', 'seriesY', idCol))

# corr results w/o gradient
if (correlationMethod != 'none') {
Expand Down Expand Up @@ -113,6 +127,7 @@ newScatterPD <- function(.dt = data.table::data.table(),

} else if (value == 'density') {

# Note, density is not implemented in production code.
density <- groupDensity(.pd, NULL, x, group, panel)
.pd <- density
veupathUtils::logWithTime('Kernel density estimate calculated from raw data.', verbose)
Expand Down Expand Up @@ -193,6 +208,9 @@ validateScatterPD <- function(.scatter, verbose) {
#' @param sampleSizes boolean indicating if sample sizes should be computed
#' @param completeCases boolean indicating if complete cases should be computed
#' @param evilMode String indicating how evil this plot is ('strataVariables', 'allVariables', 'noVariables')
#' @param idColumn character indicating the column name of the id variable in data
#' @param returnPointIds boolean indicating if any point ids should be returned with the scatterplot data.
#' This value will only be used when idColumn is present.
#' @param verbose boolean indicating if timed logging is desired
#' @return data.table plot-ready data
#' @examples
Expand Down Expand Up @@ -243,6 +261,8 @@ scattergl.dt <- function(data,
evilMode = c('noVariables', 'allVariables', 'strataVariables'),
collectionVariablePlotRef = NULL,
computedVariableMetadata = NULL,
idColumn = NULL,
returnPointIds = c(FALSE, TRUE),
verbose = c(TRUE, FALSE)) {

if (!inherits(variables, 'VariableMetadataList')) stop("The `variables` argument must be a VariableMetadataList object.")
Expand All @@ -252,6 +272,7 @@ scattergl.dt <- function(data,
completeCases <- veupathUtils::matchArg(completeCases)
evilMode <- veupathUtils::matchArg(evilMode)
verbose <- veupathUtils::matchArg(verbose)
returnPointIds <- veupathUtils::matchArg(returnPointIds)

if (!'data.table' %in% class(data)) {
data.table::setDT(data)
Expand All @@ -276,7 +297,14 @@ scattergl.dt <- function(data,
if (!yVM@dataType@value %in% c('NUMBER', 'INTEGER') & value != 'raw') {
stop('Trend lines can only be provided for numeric dependent axes.')
}
}
}

# If returnPointIds is TRUE, require that the idColumn is present in the data.
if (returnPointIds) {
if (is.null(idColumn) || !(idColumn %in% names(data))) {
stop("idColumn not found or not supplied. Supply proper idColumn if returnPointIds is TRUE.")
}
}

groupVM <- veupathUtils::findVariableMetadataFromPlotRef(variables, 'overlay')
# Decide if we should use a gradient colorscale
Expand All @@ -302,6 +330,8 @@ scattergl.dt <- function(data,
useGradientColorscale = useGradientColorscale,
overlayValues = overlayValues,
correlationMethod = correlationMethod,
idColumn = idColumn,
returnPointIds = returnPointIds,
sampleSizes = sampleSizes,
completeCases = completeCases,
inferredVarAxis = 'y',
Expand Down Expand Up @@ -357,6 +387,8 @@ scattergl.dt <- function(data,
#' @param sampleSizes boolean indicating if sample sizes should be computed
#' @param completeCases boolean indicating if complete cases should be computed
#' @param evilMode String indicating how evil this plot is ('strataVariables', 'allVariables', 'noVariables')
#' @param idColumn character indicating the column name of the id variable in data
#' @param returnPointIds boolean indicating if any point ids should be returned with the scatterplot data.
#' @param verbose boolean indicating if timed logging is desired
#' @return character name of json file containing plot-ready data
#' @examples
Expand Down Expand Up @@ -405,6 +437,8 @@ scattergl <- function(data,
sampleSizes = c(TRUE, FALSE),
completeCases = c(TRUE, FALSE),
evilMode = c('noVariables', 'allVariables', 'strataVariables'),
idColumn = NULL,
returnPointIds = c(FALSE, TRUE),
verbose = c(TRUE, FALSE)) {

verbose <- veupathUtils::matchArg(verbose)
Expand All @@ -417,6 +451,8 @@ scattergl <- function(data,
sampleSizes = sampleSizes,
completeCases = completeCases,
evilMode = evilMode,
idColumn = idColumn,
returnPointIds = returnPointIds,
verbose = verbose)

outFileName <- writeJSON(.scatter, evilMode, 'scattergl', verbose)
Expand Down
18 changes: 16 additions & 2 deletions R/class-plotdata.R
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,9 @@ newPlotdata <- function(.dt = data.table(),
#make sure lat, lon, geoAgg vars are valid plot References
variables = NULL,
useGradientColorscale = FALSE,
overlayValues = veupathUtils::BinList(),
overlayValues = veupathUtils::BinList(),
idColumn = character(),
returnPointIds = logical(),
sampleSizes = logical(),
completeCases = logical(),
inferredVarAxis = c('y', 'x'),
Expand Down Expand Up @@ -45,6 +47,17 @@ newPlotdata <- function(.dt = data.table(),
lat <- veupathUtils::findColNamesFromPlotRef(variables, 'latitude')
lon <- veupathUtils::findColNamesFromPlotRef(variables, 'longitude')

# If we ask for the point ids, ensure the column is present. Otherwise set to null.
if (!is.null(returnPointIds) && returnPointIds && length(idColumn) > 0) {
if (idColumn %in% names(.dt) && nrow(.dt) == uniqueN(.dt[[idColumn]])) {
idCol <- idColumn
} else {
idCol <- NULL
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@bobular bobular Feb 13, 2025

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Hi! Should this maybe throw an error? Seems like there will be downstream trouble if we asked for point IDs and there's no column to get them from?

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@asizemore asizemore Feb 13, 2025

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That's a good idea! I'll add it.

}
} else {
idCol <- NULL
}

isEvil <- ifelse(evilMode %in% c('allVariables', 'strataVariables'), TRUE, FALSE)
collectionVarMetadata <- veupathUtils::findCollectionVariableMetadata(variables)
isOverlayCollection <- ifelse(is.null(collectionVarMetadata), FALSE, ifelse(collectionVarMetadata@plotReference@value == 'overlay', TRUE, FALSE))
Expand Down Expand Up @@ -88,7 +101,7 @@ newPlotdata <- function(.dt = data.table(),
panel <- c(facet1, facet2)
}

myCols <- c(x, y, z, lat, lon, group, panel, geo)
myCols <- c(x, y, z, lat, lon, group, panel, geo, idCol)
.dt <- .dt[, myCols, with=FALSE]
veupathUtils::logWithTime('Identified facet intersections.', verbose)

Expand Down Expand Up @@ -204,6 +217,7 @@ newPlotdata <- function(.dt = data.table(),
if (!is.null(lon)) { .dt[[lon]] <- updateType(.dt[[lon]], 'NUMBER')}
if (!is.null(group)) { .dt[[group]] <- updateType(.dt[[group]], groupType) }
if (!is.null(panel)) { .dt[[panel]] <- updateType(.dt[[panel]], 'STRING') }
if (!is.null(idCol)) { .dt[[idCol]] <- updateType(.dt[[idCol]], 'STRING') }
veupathUtils::logWithTime('Base data types updated for all columns as necessary.', verbose)

if (!is.null(group)) {
Expand Down
6 changes: 6 additions & 0 deletions man/scattergl.Rd
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7 changes: 7 additions & 0 deletions man/scattergl.dt.Rd
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