top_abund_tableGrob: Summary top abundant tableGrobs for plots.

In calabrialab/ISAnalytics: Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

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,
  transform_by = NULL
)

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?
transform_by	Either a function or a purrr-style lambda. This function is applied to the column by before separating columns. If NULL no function is applied. Useful to modify column order in final table.

Value

A tableGrob object

See Also

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

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)

# with transform
grob <- top_abund_tableGrob(abund, transform_by = ~ as.numeric(.x))

calabrialab/ISAnalytics documentation built on Dec. 10, 2024, 10:50 p.m.