quickDMap: quickDMap

View source: R/quickDMap.R

quickDMapR Documentation

quickDMap

Description

Creates a companion heatmap for the dendrogram made by quickDendro.

Usage

quickDMap(filt_df, miRNA_exp, mRNA_exp, distmeth, hclustmeth,
pathwayname)

Arguments

filt_df

Dataframe from the matrixFilter function.

miRNA_exp

miRNA data from using the diffExpressRes function on miRNA data.

mRNA_exp

mRNA data from using the diffExpressRes function on miRNA data.

distmeth

Dist method for hierarchical clustering. Default is "maximum".

hclustmeth

Hclust method for hierarchical clustering. Default is "ward.D".

pathwayname

Character which is the name of pathway of interest. Default is "Pathway".

Value

A heatmap with time points as the x axis and genes as the y axis. Gene order will be the same as quickDendro.

Examples

library(org.Mm.eg.db)

miR <- mm_miR[1:50,]

mRNA <- mm_mRNA[1:100,]

MAE <- startObject(miR = miR, mRNA = mRNA)

MAE <- getIdsMir(MAE, assay(MAE, 1), orgDB = org.Mm.eg.db, 'mmu')

MAE <- getIdsMrna(MAE, assay(MAE, 2), "useast", 'mmusculus', orgDB = org.Mm.eg.db)

MAE <- diffExpressRes(MAE, df = assay(MAE, 1), dataType = 'Log2FC',
                     genes_ID = assay(MAE, 3),
                      idColumn = 'GENENAME',
                      name = "miRNA_log2fc")

MAE <- diffExpressRes(MAE, df = assay(MAE, 2), dataType = 'Log2FC',
                     genes_ID = assay(MAE, 7),
                     idColumn = 'GENENAME',
                     name = "mRNA_log2fc")

Filt_df <- data.frame(row.names = c("mmu-miR-145a-3p:Adamts15",
                                   "mmu-miR-146a-5p:Acy1"),
                     corr = c(-0.9191653, 0.7826041),
                     miR = c("mmu-miR-145a-3p", "mmu-miR-146a-5p"),
                     mRNA = c("Adamts15", "Acy1"),
                     miR_Entrez = c(387163, NA),
                     mRNA_Entrez = c(235130, 109652),
                     TargetScan = c(1, 0),
                     miRDB = c(0, 0),
                     Predicted_Interactions = c(1, 0),
                     miRTarBase = c(0, 1),
                     Pred_Fun = c(1, 1))

MAE <- matrixFilter(MAE, miningMatrix = Filt_df, negativeOnly = FALSE,
                   threshold = 1, predictedOnly = FALSE)

quickDendro(filt_df=MAE[[11]], miRNA_exp=MAE[[9]],
            mRNA_exp=MAE[[10]], pathwayname = "Test")

quickDMap(filt_df=MAE[[11]], miRNA_exp=MAE[[9]],
          mRNA_exp=MAE[[10]], pathwayname = "Test")

Krutik6/TimiRGeN documentation built on Jan. 27, 2024, 7:46 p.m.