fg_save_plots: Saves numerous plots for all summary statistics to a folder.

In aya49/flowGraph: Identifying differential cell populations in flow cytometry data accounting for marker frequency

Saves numerous plots for all summary statistics to a folder.

Description

Saves numerous plots for all summary statistics in a given flowGraph object to a user specified folder.

Usage

fg_save_plots(
  fg,
  plot_path,
  plot_types = "node",
  interactive = FALSE,
  adjust_custom = "byLayer",
  label_max = 10,
  box_no = 20,
  paired = FALSE,
  logged = FALSE,
  filter_adjust0 = 1,
  filter_es = 0,
  filter_btwn_tpthres = 1,
  filter_btwn_es = 0,
  overwrite = TRUE,
  node_labels = "NONE",
  ...
)

Arguments

fg	flowGraph object.
plot_path	A string indicating the folder path to where the function should save the plots.
plot_types	A string or a vector of strings indicating what feature types and their summaries the function should plot for: 'node' or 'edge'.
interactive	A logical indicating whether the QQ plot, p-value vs difference plot, and the cell hierarchy plots should be interactive; see functions fg_plot and fg_plot_qq.
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.
label_max	An integer indicating how many labels should be shown in the functions fg_plot_pVSdiff and fg_plot.
box_no	An integer indicating the maximum number of boxplots to save; used in function fg_plot_box.
paired	A logical indicating whether the summary is paired; used in function fg_plot_box.
logged	A logical indicating whether or not to log the summary statistic p value in the qq plots.
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. This parameter is used for the QQ and the pVSdifference plots.
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.
overwrite	A logical variable indicating whether or not to replace old plots if they exist under the same folder name.
node_labels	Parameter for the fg_plot function.
...	Other parameters for the fg_plot function.

Details

The interactive plots are made using the ggiraph package.

Value

No return; plots are saved to file.

See Also

flowGraph-class fg_plot plot_gr fg_get_feature fg_get_summary fg_plot_qq fg_plot_pVSdiff fg_plot_box

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_save_plots(fg, "temp")

aya49/flowGraph documentation built on Feb. 4, 2024, 6:40 p.m.