Plot EWCE results

Source: R/ewce_plot.r

ewce_plot generates plots of EWCE enrichment results

ewce_plot(
  total_res,
  mtc_method = "bonferroni",
  ctd = NULL,
  align = "v",
  rel_heights = c(0.3, 1),
  axis = "lr"
)

Arguments

total_res

results dataframe generated using bootstrap_enrichment_test or ewce_expression_data functions. Multiple results tables can be merged into one results table, as long as the 'list' column is set to distinguish them.
mtc_method

method to be used for multiple testing correction. Argument is passed to p.adjust. Valid options are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY",
ctd

Should be provided so that the dendrogram can be taken from it and added to plots
align

(optional) Specifies whether graphs in the grid should be horizontally ("h") or vertically ("v") aligned. Options are "none" (default), "hv" (align in both directions), "h", and "v".
rel_heights

(optional) Numerical vector of relative rows heights. Works just as rel_widths does, but for rows rather than columns.
axis

(optional) Specifies whether graphs should be aligned by the left ("l"), right ("r"), top ("t"), or bottom ("b") margins. Options are "none" (default), or a string of any combination of l, r, t, and b in any order (e.g. "tblr" or "rlbt" for aligning all margins). Must be specified if any of the graphs are complex (e.g. faceted) and alignment is specified and desired. See align_plots() for details.

Value

A ggplot containing the plot

Examples

## Bootstrap significance test,
##  no control for transcript length or GC content
## Use pre-computed results to speed up example
full_results <- EWCE::example_bootstrap_results()

### Skip this for example purposes
## Load the single cell data
# ctd <- ewceData::ctd()
# hits <- ewceData::example_genelist()
# full_results <- EWCE::bootstrap_enrichment_test(
#    sct_data = ctd,
#    hits = hits,
#    annotLevel = 1,
#    sctSpecies = "mouse",
#    genelistSpecies = "human"
# )

## Generate the plot
print(EWCE::ewce_plot(
    total_res = full_results$results,
    mtc_method = "BH"
))

#> Loading required namespace: cowplot
#> $plain
#>