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Visualize Comparison of an Molecule Identifier between Groups

Source: R/vis_identifier.R
vis_identifier_grp_comparison.Rd

NOTE: the dataset must be dense matrix in UCSC Xena data hubs.

Usage

vis_identifier_grp_comparison(
  dataset = NULL,
  id = NULL,
  grp_df,
  samples = NULL,
  fun_type = c("betweenstats", "withinstats"),
  type = c("parametric", "nonparametric", "robust", "bayes"),
  pairwise.comparisons = TRUE,
  p.adjust.method = c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr",
    "none"),
  ggtheme = cowplot::theme_cowplot(),
  ...
)

Arguments

dataset

the dataset to obtain identifiers.

id

the molecule identifier.

grp_df

When dataset and id are all not NULL, it should be a data.frame with 2 or 3 columns.

  • The first column refers to sample ID.

  • The second column refers to groups indicated in axis X.

  • The third column is optional, which indicates facet variable. When any of dataset and id is NULL, it should be a data.frame with 3 or 4 columns.

  • The first column refers to sample ID.

  • The second column refers to values indicated in axis Y.

  • The third column refers to groups indicated in axis X.

  • The fourth column is optional, which indicates facet variable.

samples

default is NULL, can be common sample names for two datasets.

fun_type

select the function to compare groups.

type

A character specifying the type of statistical approach:

  • "parametric"

  • "nonparametric"

  • "robust"

  • "bayes"

You can specify just the initial letter.

pairwise.comparisons

whether pairwise comparison

p.adjust.method

Adjustment method for p-values for multiple comparisons. Possible methods are: "holm" (default), "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

ggtheme

A {ggplot2} theme. Default value is ggstatsplot::theme_ggstatsplot(). Any of the {ggplot2} themes (e.g., theme_bw()), or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.). But note that sometimes these themes will remove some of the details that {ggstatsplot} plots typically contains. For example, if relevant, ggbetweenstats() shows details about multiple comparison test as a label on the secondary Y-axis. Some themes (e.g. ggthemes::theme_fivethirtyeight()) will remove the secondary Y-axis and thus the details as well.

...

other parameters passing to ggstatsplot::ggbetweenstats or ggstatsplot::ggwithinstats.

Value

a (gg)plot object.

Examples

if (FALSE) {
library(UCSCXenaTools)
expr_dataset <- "TCGA.LUAD.sampleMap/HiSeqV2_percentile"
cli_dataset <- "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
id <- "TP53"
cli_df <- XenaGenerate(
  subset = XenaDatasets == "TCGA.LUAD.sampleMap/LUAD_clinicalMatrix"
) %>%
  XenaQuery() %>%
  XenaDownload() %>%
  XenaPrepare()

# group data.frame with 2 columns
vis_identifier_grp_comparison(expr_dataset, id, cli_df[, c("sampleID", "gender")])
# group data.frame with 3 columns
vis_identifier_grp_comparison(
  expr_dataset, id,
  cli_df[, c("sampleID", "pathologic_M", "gender")] %>%
    dplyr::filter(pathologic_M %in% c("M0", "MX"))
)

# When not use the value of `identifier` from `dataset`
vis_identifier_grp_comparison(grp_df = cli_df[, c(1, 2, 71)])
vis_identifier_grp_comparison(grp_df = cli_df[, c(1, 2, 71, 111)])
}