Launch bettr app to explore and aggregate performance metrics
A data.frame
in wide format. Should contain one column
with the IDs of the entities to be compared, and one column for each
metric to use for the comparison.
Character scalar, indicating the name of the column of df
and/or idInfo
that contains IDs of the entities to be compared
(e.g., methods).
Character vector, indicating which of the
columns of df
that correspond to metrics of interest. Only metrics
included here will be displayed.
Named numeric vector providing initial weights for
each metric to use for aggregating them into a final score. Must contain
one entry per metric included in metrics
.
Named list with initial values of transformation parameters for each metric. Each list entry should correspond to one metric, and take the form of a list with up to four elements, named:
* **flip**: Logical scalar; whether or not to flip the sign of the
metric values. Defaults to `FALSE`.
* **offset**: Numeric scalar; offset to add to the (flipped)
metric values. Defaults to `0`.
* **transform**: Character scalar; one of 'None', 'z-score',
'\[0,1\]', '\[-1,1\]', 'Rank', 'Rank+\[0,1\]' or 'z-score+\[0,1\]',
indicating which transform to apply to
the metric values (after any flipping and/or adding the offset).
Defaults to 'None'.
* **cuts**: Numeric vector or `NULL`; the cut points that will
be used to bin the metric values (after the other transformations).
Defaults to `NULL`.
Only values deviating from the defaults need to be explicitly specified,
the others will be initialized to their default values.
data.frame
with annotations for metrics. Must have
a column named 'Metric' identifying the respective metrics.
Named list with colors used for columns of
metricInfo
. Should follow the format required for ComplexHeatmap
heatmap annotations. The list can include an entry named 'Metric', which
contains a named vector with colors to use for metrics.
data.frame
with annotations for entities. Must have a
column named according to idCol
identifying the respective entities.
Named list with colors used for columns of idInfo
.
Should follow the format required for ComplexHeatmap heatmap
annotations. The list can include an entry named according to idCol
,
which contains a named vector with colors to use for entities.
Numeric scalar in (0,1), giving the resolution at which weights can be specified using the sliders in the interface.
Character scalar giving the bootswatch theme for the app (see https://bootswatch.com/). Default 'darkly'.
Character scalar giving the title that will be used for the app. Defaults to 'bettr'.
A SummarizedExperiment
generated by assembleSE
. If
this is not NULL
, df
, metrics
, initialWeights
,
initialTransforms
, metricInfo
, metricColors
, idInfo
and
idColors
arguments will be ignored and the information will be
extracted from the SummarizedExperiment
object.
A shiny application
df <- data.frame(Method = c("M1", "M2", "M3"), metric1 = c(1, 2, 3),
metric2 = c(3, 1, 2), metric3 = factor(c("a", "a", "b")))
initialTransforms <- list(metric1 = list(flip = TRUE, offset = 4))
metricInfo <- data.frame(Metric = c("metric1", "metric2", "metric3"),
Group = c("G1", "G2", "G2"))
idInfo <- data.frame(Method = c("M1", "M2", "M3"),
Type = c("T1", "T1", "T2"))
metricColors <- list(Group = c(G1 = "red", G2 = "blue"))
if (interactive()) {
bettr(df = df, idCol = "Method",
metrics = c("metric1", "metric2", "metric3"),
initialTransforms = initialTransforms,
metricInfo = metricInfo, metricColors = metricColors,
idInfo = idInfo)
}