func.tilemap: Make heatmap-like tile plot. (wrapper of gplots::heatmap2)

In mrmtshmp/ExploratoryDataAnalysis: Make plots for explanatory data analyses

Description

Make heatmap-like tile plot. (wrapper of gplots::heatmap2)

Usage

func.tilemap(
  fn.output.pdf = "Tile",
  surfix.maintitle = "Group: ",
  bin = FALSE,
  n.breaks = 20,
  col.bias = 2,
  breaks = NULL,
  row.adjust = 0,
  count_table,
  physi_table,
  filt.Features = NULL,
  unitHierarchy = c("Kingdom", "Phylum", "Class", "Order", "Family", "Genus",
    "Species", "NoAgg"),
  method.dist.Row = c("manhattan", "euclidean"),
  method.hclust.Row = c("ward.D2"),
  method.dist.Col = c("manhattan", "euclidean"),
  method.hclust.Col = c("ward.D2")
)

Arguments

fn.output.pdf	<character; output> File name of PDF output.
surfix.maintitle	<character; output> Surfix of Main title in each page.
bin	<numeric; processing>
n.breaks	<numeric; processing; prefix =20>
col.bias	<numeric; processing; prefix =2> Colour brewer setting
breaks	<numeric>
row.adjust	<numeric>
count_table	<object; input data; mandatory> A data.frame with features as column and subjects as rows.
physi_table	<object; input data> A data.frame with 2 column of a feature and subject ID. This ID must be identical with of count_table.
filt.Features	<character strings; input data> Select column of count_table. If NULL, all features are selected.
unitHierarchy	<for future update...> c('Kingdom', 'Phylum', 'Class', 'Order', 'Family', 'Genus', 'Species', "NoAgg"),
method.dist.Row	= c('manhattan','euclidean'),
method.hclust.Row	= c('ward.D2'),
method.dist.Col	= c('manhattan','euclidean'),
method.hclust.Col	= c('ward.D2')

mrmtshmp/ExploratoryDataAnalysis documentation built on Oct. 6, 2020, 8 a.m.