scrna_evalPlot_silh: scrna_evalPlot_silh

Description Usage Arguments Value Examples

View source: R/scrna_plot.R

Description

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

Usage

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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

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

plger/pipeComp documentation built on Nov. 2, 2021, 8:40 p.m.