scrna_evalPlot_silh {pipeComp} | R Documentation |
Plot a min/max/mean/median silhouette width heatmap from aggregated evaluation results of the 'scrna_pipeline'.
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, ... )
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' |
A Heatmap
data("exampleResults", package="pipeComp") scrna_evalPlot_silh( exampleResults, agg.by=c("filt","norm"), row_split="norm" )