top_abund_tableGrob {ISAnalytics} | R Documentation

## Summary top abundant tableGrobs for plots.

### Description

Produce summary tableGrobs as R graphics. For this functionality the suggested package gridExtra is required. To visualize the resulting object:

    gridExtra::grid.arrange(tableGrob)

### Usage

    top_abund_tableGrob(
      df,
      id_cols = mandatory_IS_vars(),
      quant_col = "fragmentEstimate_sum_PercAbundance",
      by = "TimePoint",
      alluvial_plot = NULL,
      top_n = 10,
      tbl_cols = "GeneName",
      include_id_cols = FALSE,
      digits = 2,
      perc_symbol = TRUE
    )

### Arguments

`df` | A data frame
`id_cols` | Character vector of id column names. To plot after alluvial, these columns must be the same as the `alluvia` argument of integration_alluvial_plot.
`quant_col` | Column name holding the quantification value. To plot after alluvial, these columns must be the same as the `plot_y` argument of integration_alluvial_plot.
`by` | The column name to subdivide tables for. The function will produce one table for each distinct value in `by`. To plot after alluvial, these columns must be the same as the `plot_x` argument of integration_alluvial_plot.
`alluvial_plot` | Either NULL or an alluvial plot for color mapping between values of y.
`top_n` | Integer. How many rows should the table contain at most?
`tbl_cols` | Table columns to show in the final output besides `quant_col`.
`include_id_cols` | Logical. Include `id_cols` in the output?
`digits` | Integer. Digits to show for the quantification column
`perc_symbol` | Logical. Show percentage symbol in the quantification column?

### Value

A tableGrob object

### See Also

Other Plotting functions: `CIS_volcano_plot()`, `HSC_population_plot()`, `circos_genomic_density()`, `integration_alluvial_plot()`, `sharing_heatmap()`, `sharing_venn()`

### Examples

    data("integration_matrices", package = "ISAnalytics")
    data("association_file", package = "ISAnalytics")
    aggreg <- aggregate_values_by_key(
        x = integration_matrices,
        association_file = association_file,
        value_cols = c("seqCount", "fragmentEstimate")
    )
    abund <- compute_abundance(x = aggreg)
    grob <- top_abund_tableGrob(abund)
    gridExtra::grid.arrange(grob)

[Package ISAnalytics version 1.4.3 Index]