get_hca: get_hca

In kuppal2/xmsPANDA: R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

Description

This function performs two-way hierarchical clustering analysis and generates a heatmap showing the clustering results. The input intensity matrix could be transformed or non-transformed intensities. Sample labels in the class labels file should be in the same order as the intensity matrix or feature table.

Usage

get_hca(feature_table_file, parentoutput_dir, class_labels_file, heatmap.col.opt = "RdBu", cor.method = "spearman",
is.data.znorm = FALSE, analysismode = "classification", sample.col.opt = "rainbow", plots.width = 2000,
plots.height = 2000, plots.res = 300, alphacol = 0.3,hca_type="two-way",similarity.matrix="correlation")

Arguments

feature_table_file	Feature table that includes the mz, retention time, and measured intensity in each sample for each analyte. The first 2 columns should be the mz and time. The remaining columns should correspond to the samples in the class labels file with each column including the intensity profile of a sample. Full path required. Eg: C:/My Documents/test.txt The feature table should be in a tab-delimited format. An example of the input file is provided under the "example" folder.
parentoutput_dir	Provide full path of the folder where you want the results to be written. Eg: C:/My Documents/ProjectA/results/
class_labels_file	File with class labels information for each sample. Samples should be in the same order as in the feature table. Please use the same format as in the example folder.
heatmap.col.opt	Color scheme for HCA hetmap eg: "RdBu", "topo", "heat", or "terrain"
cor.method	Correlation method. Options: "person" or "spearman". Default: "spearman"
is.data.znorm	Is the data already auto-scaled or z-scaled? eg: TRUE or FALSE
analysismode	"classification" for group-wise comparison (case vs control) or "regression" for continuous response variables. Default: "classification"
sample.col.opt	Color scheme for PCA and heatmap sample axis eg: "heat" or "topo" or "rainbow"
plots.width	Width of the tiff file. eg: 2000
plots.height	Height of the tiff file. eg: 2000
plots.res	Resolution of the tiff file. eg: 300
alphacol	Color scaling parameter eg:0.3
hcatype	Color scaling parameter eg:"two-way" or "one-way"
similarity.matrix	Correlation or topological overlap matrix eg:"correlation" or "TOM"

Value

Heatmap from Two-way hierarchical clustering analysis; Intensity matrix in the same order as the dendrograms in heatmap; Sample cluster labels

Author(s)

Karan Uppal <[e-mail]>

kuppal2/xmsPANDA documentation built on May 15, 2021, 5:48 a.m.