gridplot: Fingerprint grid visualization

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

Description

The gridplot function will generate a grid plot as a pdf file. Specific working directory for the analysis need to be specified for saving the file. The result of the plot should be return in the same working directory. The default cut off for visualization is set at 15%, it can be changed to any value between 0-100%.

Usage

gridplot(Group_df, cutoff = NULL, Ref_group = NULL, filename = NULL)

Arguments

Group_df	Dataframe with output generated after running the'Groupcomparison' function
cutoff	Numeric value specifying the percentage cut off used for fingerprint visualization (from 0 to 100)
Ref_group	Character vector specifying value within the group column that will be used as Reference group
filename	Character vector with a name for saving file

Value

       A pdf file of grid plot

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"]]
Group_df = Groupcomparison(GSE13015, sample_info = NULL,
                          FC = 0, pval = 0.1, FDR = TRUE, Test_group = "Sepsis",
                          Group_column = "Group_test", Ref_group = "Control")
gridplot(Group_df, cutoff = 15,
         Ref_group = "Control",
         filename= tempfile())

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