Create a summary heatmap. The input arguments for this functions are
typically generated using bettrGetReady
, which ensures that
all required columns are available.
makeHeatmap(
bettrList = NULL,
plotdata,
scoredata,
idCol,
metricCol = "Metric",
valueCol = "ScaledValue",
weightCol = "Weight",
scoreCol = "Score",
metricGroupCol = "metricGroup",
metricInfo,
metricColors,
idInfo,
idColors,
metricCollapseGroup = FALSE,
metricGrouping = "---",
labelSize = 10,
showRowNames = TRUE,
plotType = "Heatmap",
rownamewidth_cm = 6,
colnameheight_cm = 6
)
A list
, the output object from prepData
.
If bettrList
is provided, arguments plotdata
,
scoredata
, idCol
, metricCol
, valueCol
,
weightCol
, scoreCol
, metricGroupCol
,
metricInfo
, metricColors
, idInfo
, idColors
,
metricCollapseGroup
, metricGrouping
and methods
will be ignored and the corresponding values will be extracted from
bettrList
. This is the recommended way of calling the plotting
functions, as it ensures compatibility of all components.
A data.frame
with columns representing methods,
metrics, scores, and weights. Typically obtained as
prepData$plotdata
, where prepData
is the output from
bettrGetReady
.
A data.frame
with columns representing methods,
aggregated scores, and any other method annotations. Typically
obtained as prepData$scoredata
, where prepData
is the
output from bettrGetReady
.
Character scalar indicating which column of plotdata
and
scoredata
contains the method IDs.
Character scalar indicating which column of plotdata
contains the metric IDs. Typically, "Metric"
.
Character scalar indicating which column of plotdata
contains the metric values. Typically, "ScaledValue"
.
Character scalar indicating which column of plotdata
contains the weight values. Typically, "Weight"
.
Character scalar indicating which column of scoredata
contains the aggregated score values. Typically, "Score"
.
Character scalar indicating which column of
plotdata
contains the information about the metric group.
Typically, "metricGroup"
.
data.frame
with annotations for metrics. Typically
obtained as prepData$metricInfo
, where prepData
is the
output from bettrGetReady
.
Named list with colors used for the metrics and
any other metric annotations. Typically obtained as
prepData$metricColors
, where prepData
is the output from
bettrGetReady
.
data.frame
with annotations for entities. Typically
obtained as prepData$idInfo
, where prepData
is the
output from bettrGetReady
.
Named list with colors used for methods and any other
method annotations. Typically obtained as prepData$idColors
,
where prepData
is the output from bettrGetReady
.
Logical scalar indicating whether metrics
should be collapsed by the group variable provided by
metricGrouping
. Typically obtained as
prepData$metricCollapseGroup
, where prepData
is the
output from bettrGetReady
.
Character scalar indicating the column of
metricInfo
that was used to group metrics. Typically obtained as
prepData$metricGrouping
, where prepData
is the output
from bettrGetReady
.
Numeric scalar providing the size of the labels in the plot.
Logical scalar indicating whether to show row (method) names in the heatmap.
Either "Heatmap"
or "Dot plot"
indicating the
type of plot to construct.
Numeric scalars defining the width of row names and height of column names, in cm.
A HeatmapList
object.
## Generate example data
df <- data.frame(Method = c("M1", "M2", "M3"),
metric1 = c(1, 2, 3),
metric2 = c(3, 1, 2))
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"))
prepData <- bettrGetReady(df = df, idCol = "Method",
metricInfo = metricInfo, idInfo = idInfo)
makeHeatmap(bettrList = prepData, plotType = "Heatmap")
makeHeatmap(bettrList = prepData, plotType = "Dot plot")