Description Usage Arguments Details Author(s)

Function is modification of function `heatmap.2`

from package gplots

1 | ```
metaheat2(x, Rowv = TRUE, Colv = if (symm) "Rowv" else TRUE, distfun = dist, hclustfun = hclust, dendrogram = c("both", "row", "column", "none"), symm = FALSE, scale = c("none", "row", "column"), na.rm = TRUE, revC = identical(Colv, "Rowv"), add.expr, breaks, symbreaks = min(x < 0, na.rm = TRUE) || scale != "none", col = "heat.colors", colsep, rowsep, sepcolor = "white", sepwidth = c(0.05, 0.05), cellnote, notecex = 1, notecol = "cyan", na.color = par("bg"), trace = c("column", "row", "both", "none"), tracecol = "cyan", hline = median(breaks), vline = median(breaks), linecol = tracecol, margins = c(5, 5), ColSideColors, RowSideColors, cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 + 1/log10(nc), labRow = NULL, labCol = NULL, key = TRUE, keysize = 1.5, density.info = c("histogram", "density", "none"), denscol = tracecol, symkey = min(x < 0, na.rm = TRUE) || symbreaks, densadj = 0.25, main = NULL, xlab = NULL, ylab = NULL, lmat = NULL, lhei = NULL, lwid = NULL, legend.names, discrete = FALSE, horiz=TRUE, ...)
``` |

`x` |
numeric matrix of the values to be plotted. |

`Rowv` |
determines if and how the row dendrogram should be reordered. By default, it is TRUE, which implies dendrogram is computed and reordered based on row means. If NULL or FALSE, then no dendrogram is computed and no reordering is done. If a |

`Colv` |
determines if and how the column dendrogram should be reordered. Has the options as the Rowv argument above and additionally when x is a square matrix, |

`distfun` |
function used to compute the distance (dissimilarity) between both rows and columns. Defaults to |

`hclustfun` |
function used to compute the hierarchical clustering when Rowv or Colv are not dendrograms. Defaults to |

`dendrogram` |
character string indicating whether to draw 'none', 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning is issued and Rowv (or Colv) arguments are honoured. |

`symm` |
logical indicating if x should be treated symmetrically; can only be true when x is a square matrix. |

`scale` |
character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default is |

`na.rm` |
logical indicating whether NA's should be removed. |

`revC` |
logical indicating if the column order should be |

`add.expr` |
expression that will be evaluated after the call to |

`breaks` |
(optional) Either a numeric vector indicating the splitting points for binning x into colors, or a integer number of break points to be used, in which case the break points will be spaced equally between |

`symbreaks` |
Boolean indicating whether breaks should be made symmetric about 0. Defaults to |

`col` |
colors used for the image. Defaults to heat colors ( |

`colsep, rowsep, sepcolor` |
(optional) vector of integers indicating which columns or rows should be separated from the preceding columns or rows by a narrow space of color |

`sepwidth` |
(optional) Vector of length 2 giving the width (colsep) or height (rowsep) the separator box drawn by colsep and rowsep as a function of the width (colsep) or height (rowsep) of a cell. Defaults to |

`cellnote` |
(optional) matrix of character strings which will be placed within each color cell, e.g. p-value symbols. |

`notecex` |
(optional) numeric scaling factor for |

`notecol` |
(optional) character string specifying the color for |

`na.color` |
Color to use for missing value ( |

`trace` |
character string indicating whether a solid "trace" line should be drawn across 'row's or down 'column's, 'both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'column'. |

`tracecol` |
character string giving the color for "trace" line. Defaults to "cyan". |

`hline, vline, linecol` |
Vector of values within cells where a horizontal or vertical dotted line should be drawn. The color of the line is controlled by linecol. Horizontal lines are only plotted if trace is 'row' or 'both'. Vertical lines are only drawn if trace 'column' or 'both'. hline and vline default to the median of the breaks, linecol defaults to the value of tracecol. |

`margins` |
numeric vector of length 2 containing the margins (see |

`ColSideColors` |
(optional) character vector of length |

`RowSideColors` |
(optional) character vector of length |

`cexRow, cexCol` |
positive numbers, used as |

`labRow, labCol` |
character vectors with row and column labels to use; these default to |

`key` |
logical indicating whether a color-key (legend) should be shown. |

`keysize` |
numeric value indicating the size of the key |

`density.info` |
character string indicating whether to superimpose a 'histogram', a 'density' plot, or no plot ('none') on the color-key. |

`denscol` |
character string giving the color for the density display specified by |

`symkey` |
Boolean indicating whether the color key should be made symmetric about 0. Defaults to |

`densadj` |
Numeric scaling value for tuning the kernel width when a density plot is drawn on the color key. (See the |

`main, xlab, ylab` |
main, x- and y-axis titles; defaults to none. |

`lmat, lhei, lwid` |
visual layout: position matrix, column height, column width. See below for details |

`legend.names` |
character vector with labels of categories - used in legend |

`discrete` |
Logical, when |

`horiz` |
Logical, when |

`...` |
additional arguments passed on to |

See function `heatmap.2`

in gplots package for details

Ivana Ihnatova

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