heat_vis: Using correlation information to draw a heatmaps

In AllenTiTaiWang/anamiR: An integrated analysis package of miRNA and mRNA expression data

Description

This function would base on Fold-Change information from the output of negative_cor, differExp_discrete and show heatmaps to users. Note that if miRNA-gene interactions (row) from input are larger than 100, the lable in plot would be unclear.

Usage

heat_vis(cor_data, mrna_d, mirna_21)

Arguments

cor_data	matrix format generated from negative_cor.
mrna_d	differential expressed data in data.frame format, with sample name in columns and gene symbol in rows, which is generated by differExp_discrete or differExp_continuous.
mirna_21	differential expressed data in data.frame format, with sample name in columns and miRNAl in rows, which is generated by differExp_discrete or differExp_continuous, miRNA should be miRBase 21 version now.

Value

heatmap plots of miRNA and gene.

See Also

heatmap.2 for plot.

Examples

## Use the internal dataset
data("mirna", package = "anamiR", envir = environment())
data("pheno.mirna", package = "anamiR", envir = environment())
data("mrna", package = "anamiR", envir = environment())
data("pheno.mrna", package = "anamiR", envir = environment())

## SummarizedExperiment class
require(SummarizedExperiment)
mirna_se <- SummarizedExperiment(
 assays = SimpleList(counts=mirna),
 colData = pheno.mirna)

## SummarizedExperiment class
require(SummarizedExperiment)
mrna_se <- SummarizedExperiment(
 assays = SimpleList(counts=mrna),
 colData = pheno.mrna)

## Finding differential miRNA from miRNA expression data with t.test
mirna_d <- differExp_discrete(
   se = mirna_se,
   class = "ER",
   method = "t.test"
)

## Finding differential mRNA from mRNA expression data with t.test
mrna_d <- differExp_discrete(
   se = mrna_se,
   class = "ER",
   method = "t.test"
)

## Convert annotation to miRBse 21
mirna_21 <- miR_converter(data = mirna_d, original_version = 17)

## Correlation
cor <- negative_cor(mrna_data = mrna_d, mirna_data = mirna_21)

## Draw heatmap
heat_vis(cor, mrna_d, mirna_21)

AllenTiTaiWang/anamiR documentation built on May 5, 2019, 4:55 a.m.