scrna_evalPlot_silh {pipeComp} | R Documentation

## scrna_evalPlot_silh

### 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 “minSilWidth”, “meanSilWidth” (default), “medianSilWidth”, or “maxSilWidth”.
`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" )

[Package pipeComp version 1.4.0 Index]