heatmapOutput: Generate heatmaps for various studies/subgroups of a study.
In cbaf: Automated functions for comparing various omic data from cbioportal.org

Description Usage Arguments Details Value Author(s) Examples

This function can prepare heatmap for 'frequency percentage', 'mean value' and 'median value' data provided by automatedStatistics() function.

heatmapOutput(submissionName, shortenStudyNames = TRUE,
  geneLimit = FALSE, rankingMethod = "variation", heatmapFileFormat = "TIFF",
  resolution = 600, RowCex = "auto", ColCex = "auto",
  heatmapMargines = "auto", rowLabelsAngle = 0, columnLabelsAngle = 45,
  heatmapColor = "RdBu", reverseColor = TRUE, transposedHeatmap = FALSE,
  simplifyBy = FALSE, genesToDrop = FALSE)

`submissionName`	a character string containing name of interest. It is used for naming the process.
`shortenStudyNames`	a logical vector. If the value is set as TRUE, function will try to remove the last part of the cancer names aiming to shorten them. The removed segment usually contains the name of scientific group that has conducted the experiment.
`geneLimit`	if large number of genes exist in at least one gene group, this option can be used to limit the number of genes that are shown on heatmap. For instance, `geneLimit=50` will limit the heatmap to 50 genes that show the most variation across multiple study / study subgroups. The default value is `FALSE`.
`rankingMethod`	a character value that determines how genes will be ranked prior to drawing heatmap. `"variation"` orders the genes based on unique values in one or few cancer studies while `"highValue"` ranks the genes when they cotain high values in multiple / many cancer studies. This option is useful when number of genes are too much so that user has to limit the number of genes on heatmap by `geneLimit`.
`heatmapFileFormat`	This option enables the user to select the desired image file format of the heatmaps. The default value is `"TIFF"`. Other suppoeted formats include `"PNG"`, `"BMP"`, and `"JPG"`.
`resolution`	a number. This option can be used to adjust the resolution of the output heatmaps as 'dot per inch'. The defalut value is 600.
`RowCex`	a number that specifies letter size in heatmap row names, which ranges from 0 to 2. If `RowCex = "auto"`, the function will automatically determine the best RowCex.
`ColCex`	a number that specifies letter size in heatmap column names, which ranges from 0 to 2. If `ColCex = "auto"`, the function will automatically determine the best ColCex.
`heatmapMargines`	a numeric vector that is used to set heatmap margins. If `heatmapMargines = "auto"`, the function will automatically determine the best possible margines. Otherwise, enter the desired margine as e.g. c(10,10.)
`rowLabelsAngle`	a number that determines the angle with which the gene names are shown in heatmaps. The default value is 0 degree.
`columnLabelsAngle`	a number that determines the angle with which the studies/study subgroups names are shown in heatmaps. The default value is 45 degree.
`heatmapColor`	a character string that defines heatmap color. The default value is `'RdBu'`. `'RdGr'` is also a popular color in genomic studies. To see the rest of colors, please type `library(RColorBrewer)` and then `display.brewer.all()`.
`reverseColor`	a logical value that reverses the color gradiant for heatmap(s).
`transposedHeatmap`	a logical value that transposes heatmap rows to columns and vice versa.
`simplifyBy`	a number that tells the function to change the values smaller than that to zero. The purpose behind this option is to facilitate recognizing candidate genes. Therefore, it is not suited for publications. It has the same unit as `cutoff`.
`genesToDrop`	a character vector. Gene names within this vector will be omitted from heatmap.The default value is `FALSE`.

Package:	cbaf
Type:	Package
Version:	1.12.1
Date:	2020-12-07
License:	Artistic-2.0

Based on preference, three heatmaps for "Frequency.Percentage" , "Mean.Value" and "Median.value" can be generated. If more than one group of genes are entered, output for each group will be strored in a separate sub-directory.

Arman Shahrisa, shahrisa.arman@hotmail.com [maintainer, copyright holder]

Maryam Tahmasebi Birgani, tahmasebi-ma@ajums.ac.ir

genes <- list(K.demethylases = c("KDM1A", "KDM1B", "KDM2A", "KDM2B", "KDM3A",
 "KDM3B", "JMJD1C", "KDM4A"), K.methyltransferases = c("SUV39H1", "SUV39H2",
 "EHMT1", "EHMT2", "SETDB1", "SETDB2", "KMT2A", "KMT2A"))

obtainOneStudy(genes, "test", "Breast Invasive Carcinoma (TCGA, Cell 2015)",
"RNA-Seq", desiredCaseList = c(3,4))

automatedStatistics("test", obtainedDataType = "single study", calculate =
c("frequencyPercentage", "frequencyRatio"))

heatmapOutput(submissionName = "test")