heat_vis {anamiR} | R Documentation

## Using correlation information to draw a heatmaps

### 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)

[Package anamiR version 1.8.0 Index]