plotCorrelation: Plot correlations

Description Usage Arguments Value Examples

Description

Plot the correlation of a miRNA and mRNA with their linear regression

Usage

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plotCorrelation(obj, miRNA, mRNA, type = "cor", samples = "all",
  col.color = 1, i.legend = !is.na(col.color), pos.legend = "topright",
  sample.names = FALSE, pos.sample.names = 1, cex.main = 1.35,
  alternative = "two.sided", colors = c("turquoise", "violet"))

Arguments

obj

corObject

miRNA

character, miRNA selected

mRNA

character, mRNA selected

type

"cor" or "residuals"

samples

colunm name of the pheno.miRNA where to look for the grouping factor. The column must contain character names.

col.color

name of the column in the pheno slot used for coloring the samples.

i.legend

TRUE or FALSE. Plot legend

pos.legend

set the legend position from legend ‘"bottomright"’, ‘"bottom"’, ‘"bottomleft"’, ‘"left"’, ‘"topleft"’, ‘"top"’, ‘"topright"’, ‘"right"’ and ‘"center"’.

sample.names

TRUE or FALSE. Plot text of sample names.

pos.sample.names

Position of the text for sample names from text. Values of ‘1’, ‘2’, ‘3’ and ‘4’, respectively indicate positions below, to the left of, above and to the right of the specified coordinates.

cex.main

cex parameter for the main title.

alternative

alternative hypotheses used for computing the p value of the correlation. One of "two.sided", "less","greater".

colors

In case of a two-level factor grouping, colors to be used.

Value

A scatter plot showing the correlation of the miRNA and mRNA expression of a miRNA-mRNA pair. A line representing the linear regression between both variables is also plotted.

Examples

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data(data.obj)
plotCorrelation(data.obj, miRNA="hsa-miR-107", mRNA="ACPP",
 type="cor", col.color="group", sample.names=TRUE)
plotCorrelation(data.obj, miRNA="hsa-miR-107", mRNA="ACPP",
 type="residuals")

mariavica/mircomb documentation built on Feb. 3, 2020, 2:28 a.m.