plotHeatmapTable: plot a table with colour indicated

In nickytong/GenAnalysis: Genomic Analysis

Description

Given a table object, this function plot the count and indicate the actual count

Usage

plotHeatmapTable(x, y, xlab, ylab, tag = NULL, main = NULL,
  verbose = TRUE, OrdReg = TRUE, plot = TRUE, plotType = "stdres",
  low.color = "white", high.color = "blue", text.size = 8,
  stdres_range = c(-4, 4))

Arguments

x	a factor
y	a factor
xlab	xlab
ylab	ylab
tag	the tag on the title; a fisher exact test p value will be appended
verbose	logical indicating whether print model fitting result on screen
OrdReg	logical indicating if an ordinal regression is to be fitted
plot	logical indicating if a plot is to be generated
plotType	type of plot. stdres for coloring by std residuals. count for coloring by count. dull for no coloring
low.color	the color for smallest value
high.color	the color for largest value
text.size	text size for the count

Details

modified on 2014/01/29: fisher test might fail; add try-catch (i.e. user chisq or NA); default xlab is related to tab dimnames now. modified on 2014/01/30: add ordinal logistic regression info modified on 2014/11/26: when chisq is successfully fitted, cell will be colored by standardized residual to understand which cell is enriched

Examples

x <- sample(LETTERS[1:4], 100, replace=TRUE)
y <- sample(LETTERS[5:8], 100, replace=TRUE)

nickytong/GenAnalysis documentation built on July 20, 2019, 8:57 a.m.