iobr_cor_plot: Integrative correlation between phenotype and features
In IOBR/IOBR: Immune Oncology Biological Research

iobr_cor_plot

R Documentation

Integrative correlation between phenotype and features

Description

Integrative correlation between phenotype and features

Usage

iobr_cor_plot(
  pdata_group,
  id1 = "ID",
  feature_data,
  id2 = "ID",
  target = NULL,
  group = "group3",
  is_target_continuous = TRUE,
  padj_cutoff = 1,
  index = 1,
  category = "signature",
  signature_group = sig_group,
  ProjectID = "TCGA",
  palette_box = "nrc",
  cols_box = NULL,
  palette_corplot = "pheatmap",
  palette_heatmap = 2,
  feature_limit = 26,
  character_limit = 60,
  show_heatmap_col_name = FALSE,
  show_col = FALSE,
  show_plot = FALSE,
  path = NULL,
  discrete_x = 20,
  discrete_width = 20,
  show_palettes = FALSE,
  fig.type = "pdf"
)

Arguments

`pdata_group`	A data frame to be analyzed, including id1 and phenotype data
`id1`	column of identifier to pdata
`feature_data`	A data frame which should contain the feature data.
`id2`	column of identifier of feature data
`target`	default is NULL, column of target variables if target is continuous
`group`	The grouping variable, default is "group3".
`is_target_continuous`	logical variable, if TRUE, new group will be generated based on the average or the third percentile
`padj_cutoff`	cutoff of adjust p-value to filter features when number of features is larger than 'feature_limit'
`index`	index use to order the file name
`category`	'signature' or 'gene'
`signature_group`	for signature group： 'sig_group', for gene_group 'signature_collection' or 'signature_tme'
`ProjectID`	names to define the file names
`palette_box`	palette for box plot
`cols_box`	Color settings for the box, default is NULL.
`palette_corplot`	palette for cor-plot
`palette_heatmap`	palette for heat map
`feature_limit`	The limitation of a feature, default is 26.
`character_limit`	The limitation of a character, default is 60.
`show_heatmap_col_name`	A logical value to indicate if heatmap column names should be displayed, default is FALSE.
`show_col`	A logical value to determine if the color should be shown, default is FALSE.
`show_plot`	logical variable, if TRUE, plots will be print
`path`	The path for output file storing, default is NULL.
`discrete_x`	if maximal character length of variables is larger than discrete_x, label will be discrete
`discrete_width`	numeric, default is 30, range from 20 to 80.
`show_palettes`	default is FALSE
`fig.type`	default is pdf, if not, figure will be saved in png format.