fingerprintplot: Individual fingerprint visualization The fingerprintplot...

In Drinchai/BloodGen3Module: This R package for performing module repertoire analyses and generating fingerprint representations

Description

Individual fingerprint visualization The fingerprintplot function will generate fingerprint heatmap plots as a pdf file. The file will be saved in the working directory specified for the analysis. The default cut off for visualization is set at 15%, it can be changed to any value between 0-100%.

Usage

fingerprintplot(
  Individual_df,
  sample_info = NULL,
  cutoff = NULL,
  rowSplit = TRUE,
  Ref_group = NULL,
  show_ref_group = FALSE,
  Group_column = NULL,
  Aggregate = NULL,
  filename = NULL,
  height = NULL,
  width = NULL
)

Arguments

Individual_df	Dataframe with output generated after running the 'Individualcomparison' function
sample_info	A dataframe with sample annotation.
cutoff	Numeric value specifying the percentage cut off used for fingerprint visualization ( 0 to 100).
rowSplit	Logical operator (TRUE/FALSE) to indicate if rows of the heatmaps should be split by each aggregate
Ref_group	Characters name of reference group or samples that considered as control
show_ref_group	Character vector specifying value within the group column that will be used as Reference group
Group_column	Name of the columns for the groups used for the analysis
Aggregate	Character vector specifying name of specific module aggregates for heatmap fingerprint plot
filename	Character vector with a name for saving file
height	Sets the height of the graphics region in inches. The default values are 28
width	Sets the width of the graphics region in inches. The default values are 17

Value

A heatmap of % of module response in each single sample

Author(s)

Darawan Rinchai [e-mail]

Examples

## data could be downloaded from ExperimentHub("GSE13015")
library(ExperimentHub)
library(SummarizedExperiment)
dat = ExperimentHub()
res = query(dat , "GSE13015")
GSE13015 = res[["EH5429"]]
Individual_df = Individualcomparison(GSE13015, sample_info = NULL,
                                    FC = 1.5, DIFF = 10, Group_column = "Group_test",
                                    Ref_group = "Control")
fingerprintplot(Individual_df, sample_info = NULL,
               cutoff = 15, rowSplit = TRUE, Ref_group = "Control",
               show_ref_group = FALSE, Group_column = "Group_test",
               Aggregate = c("A28"), filename = tempfile(), height = 5,
               width = 10)

Drinchai/BloodGen3Module documentation built on Sept. 20, 2021, 10:31 p.m.