plotModuleGO: Plot extracted results from module-based GO enrichment...
In ryananeff/DGCA: Differential Gene Correlation Analysis

Description Usage Arguments Value

Takes a data frame of enrichment results in multiple modules and plots the results. Note that if a GO term enrichment does not exist for that module, it is set as 0 for an OR or 1 for a p-value.

plotModuleGO(df, nTerms = 5, termVector = NULL, modules = NULL,
  heatmapColor = NULL, plotOR = FALSE, axis_text_col = "black",
  axis_x_text_angle = 45, text_size = 10, guide_title = NULL,
  coord_flip = FALSE, adjust = TRUE)

`df`	The data frame of term enrichments to be plotted.
`nTerms`	The number of terms for each module whose GO terms with the minimum enrichment p-values for that group should be plotted.
`termVector`	Optional character vector of GO term strings to plot, overriding other options.
`modules`	Optional, a list of module names to plot. Optional; if not inputted, all of the module names in the data frame will be used.
`heatmapColor`	Optional specification of the heatmap colors. If not specified, ?heat.colors will be used.
`plotOR`	Logical, indicating whether odds ratios should be plotted on the heatmap, instead of -log10 p-values (the default).
`axis_text_col`	Color of axis text.
`axis_x_text_angle`	Angle of x-axis text.
`text_size`	Text size of axes and legend in plot.
`guide_title`	Optionally, specify the title of legend.
`coord_flip`	Whether the coordinates should be flipped.
`adjust`	If p-values are plotted, whether or not the enrichment p-values from each module should be adjusted by the Benjamini-Hochberg method.

A data frame summarizing the GO term enrichments from each group, with columns on the ordered by the minimum p-value for OR term enrichment in any group.

ryananeff/DGCA documentation built on June 13, 2019, 12:57 a.m.