scrna_evalPlot_silh: scrna_evalPlot_silh

In pipeComp: pipeComp pipeline benchmarking framework

Description

Plot a min/max/mean/median silhouette width heatmap from aggregated evaluation results of the 'scrna_pipeline'.

Usage

scrna_evalPlot_silh(
  res,
  what = c("minSilWidth", "meanSilWidth"),
  step = "dimreduction",
  dims = 1,
  agg.by = NULL,
  agg.fn = mean,
  filterExpr = NULL,
  value_format = "",
  reorder_rows = FALSE,
  reorder_columns = TRUE,
  show_heatmap_legend = TRUE,
  show_column_names = FALSE,
  col = rev(RColorBrewer::brewer.pal(n = 11, "RdBu")),
  font_factor = 0.9,
  row_split = NULL,
  shortNames = TRUE,
  value_cols = c("white", "black"),
  title = NULL,
  anno_legend = TRUE,
  ...
)

Arguments

res	Aggregated pipeline results (i.e. the output of 'runPipeline' or 'aggregateResults')
what	What metric to plot, possible values are <e2><80><9c>minSilWidth<e2><80><9d>, <e2><80><9c>meanSilWidth<e2><80><9d> (default), <e2><80><9c>medianSilWidth<e2><80><9d>, or <e2><80><9c>maxSilWidth<e2><80><9d>.
step	Name of the step for which to plot the evaluation results. Defaults to "dimreduction".
dims	If multiple sets of dimensions are available, which one to use (defaults to the first).
agg.by	Aggregate results by these columns (default no aggregation)
agg.fn	Function for aggregation (default mean)
filterExpr	An optional filtering expression based on the columns of the target dataframe, (e.g. 'filterExpr=param1=="value1"').
value_format	Format for displaying cells' values (no label by default)
reorder_rows	Whether to sort rows (default FALSE). The row names themselves can also be passed to specify an order, or a 'ComplexHeatmap'.
reorder_columns	Whether to sort columns (default TRUE).
show_heatmap_legend	Passed to 'Heatmap' (default FALSE)
show_column_names	Passed to 'Heatmap' (default FALSE)
col	Colors for the heatmap
font_factor	A scaling factor applied to fontsizes (default 1)
row_split	Optional column (included in 'agg.by') by which to split the rows. Alternatively, an expression using the columns (retained after aggregation) can be passed.
shortNames	Logical; whether to use short row names (with only the parameter values instead of the parameter name and value pairs), default TRUE.
value_cols	A vector of length 2 indicating the colors of the values (above and below the mean), if printed
title	Plot title
anno_legend	Logical; whether to plot the legend for the datasets
...	Passed to 'Heatmap'

Value

A Heatmap

Examples

data("exampleResults", package="pipeComp")
scrna_evalPlot_silh( exampleResults, agg.by=c("filt","norm"), 
                     row_split="norm" )

pipeComp documentation built on Nov. 8, 2020, 7:35 p.m.