fg_plot_qq {flowGraph} | R Documentation

## Creates a QQ plot of a summary statistic.

### Description

Creates a QQ plot of a summary statistic.

### Usage

    fg_plot_qq(
      fg,
      type = "node",
      index = 1,
      summary_meta = NULL,
      adjust_custom = "byLayer",
      logged = TRUE,
      p_thres = 0.05,
      filter_adjust0 = 1,
      filter_es = 0,
      filter_btwn_tpthres = 1,
      filter_btwn_es = 0,
      shiny_plot = FALSE,
      main = NULL,
      interactive = FALSE,
      path = NULL
    )

### Arguments

`fg` | flowGraph object.
`type` | A string indicating feature type the summary was created for 'node' or 'edge'.
`index` | The user must provide `type` and additionally, one of `summary_meta` or `index`. `index` is an integer indicating the row in `fg_get_summary_desc(<flowGraph>)` of the corresponding type and summary the user would like to retrieve.
`summary_meta` | The user must provide `type` and additionally, one of `summary_meta` or `index`. `summary_meta` is a list containing `feature` (feature name), `test_name` (summary statistic name), `class` (class), `label1`, and `label2` (class labels compared). See `fg_get_summary_desc` for details.
`adjust_custom` | A function or a string indicating the test adjustment method to use. If a string is provided, it should be one of `c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")` (see `p.adjust.methods`). If a function is provided, it should take as input a numeric vector and output the same vector adjusted.
`logged` | A logical indicating whether or not to log the summary statistic p value.
`p_thres` | A double indicating a summary statistic threshold e.g. if we are plotting a T-test summary statistic, we can set the threshold to .05; nodes with a p-value greater than .05 will not be plotted.
`filter_adjust0` | A numeric variable indicating what percentage of SpecEnr values compared (minimum) should be not close to 0. Set to 1 to not conduct filtering.
`filter_es` | A numeric variable between 0 and 1 indicating what the Cohen's D value of the nodes/edges in question must be greater or equal to, to be significant.
`filter_btwn_tpthres` | A numeric variable between 0 and 1 indicating the unadjusted T-test p-value threshold used to test whether the actual and expected feature values used to calculate the specified SpecEnr feature are significantly different for each sample class. Note this only needs to be specified for SpecEnr features. Combined with `filter_btwn_es`, we conduct three tests to understand if there is an actual large difference between actual and expected features: (1,2) T-test of significance between the actual and expected raw feature value (e.g. proportion) for samples in each of the compared classes, (3) and the T-test of significance between the differences of actual and expected feature values of the two classes. If any two of the three tests come out as insignificant, we set the p-value for the associated node/edge to 1.
`filter_btwn_es` | A numeric variable between 0 and 1 indicating what the Cohen's D value of the nodes/edges in question must be greater or equal to, to be significant – see `filter_btwn_tpthres`.
`shiny_plot` | A logical indicating whether this plot is made for shiny; users don't need to change this.
`main` | A string or the title of the plot; if left as `NULL`, a default title will be applied.
`interactive` | A logical indicating whether or not plot should be an interactive ggiraph plot as opposed to a static plot.
`path` | A string indicating the path to where the function should save the plot; leave as `NULL` to not save the plot. Static plots are saved as PNG, interactive plots are saved as HTML.

### Details

The interactive plot is made using the `ggiraph` package.

### Value

A static or interactive qq plot.

### See Also

`flowGraph-class` `fg_plot` `plot_gr` `fg_get_feature` `fg_get_summary`

### Examples

     no_cores <- 1
     data(fg_data_pos2)
     fg <- flowGraph(fg_data_pos2$count, class=fg_data_pos2$meta$class,
                     no_cores=no_cores)

     fg_plot_qq(fg, type="node", summary_meta=NULL, adjust_custom="byLayer", index=1,
             interactive=TRUE, logged=FALSE)

     fg_plot_qq(fg, type="node", summary_meta=NULL, adjust_custom="byLayer", index=1,
             interactive=FALSE, logged=FALSE)

[Package flowGraph version 1.2.0 Index]