Usage
draw.boxes(slice, start, end, maxElements = 50, maxDepth = 100, label = TRUE,
labelStrand = FALSE, labelCex = 1, labelSrt = 0, labelAdj = "center",
labelOverflow = TRUE, labelFamily = "sans", colorVal = "#BBBBBB",
colorFun = function() NULL, border = "#666666", cex.lab = 1, spacing = 0.2,
bty = "o", groupBy = NA, groupPosition = NA, groupSize = NA, groupLwd = 1, ...)Arguments
slice
A data.frame holding the data to plot, with elements in rows and data in columns.
start
Single integer value, the left boundary of the window, in base pairs.
end
Single integer value, the right boundary of the window, in base pairs.
maxElements
Single integer value, the maximum amount of boxes on the plot (if exhausted, only the amount of elements will be ploted).
maxDepth
Single integer value, the maximum amount of box heights allowed on the plot to avoid overlaps (if exhausted an error message will be ploted, turning label to FALSE might help).
label
Single logical value, whether to print labels on boxes or not.
labelStrand
Single logical value, whether to add the strand at the end of labels or not.
labelCex
Single numeric value, character expansion factor for labels.
labelSrt
Single numeric value, string rotation angle for labels.
labelAdj
'left', 'right' or 'center', the horizontal adjustement of the labels on the boxes.
labelOverflow
Single logical value, whether to write labels on boxes too narrow to host them or not.
labelFamily
Single character value, the font family to use for labels ('serif', 'sans', 'mono' or 'Hershey'). 'serif' and 'sans' are not monospaced fonts, so label box sizes and collision handling might not work as expected with them.
colorVal
The color to fill boxes with (as a name, an integer or an hexadecimal character description).
colorFun
A function with no arguments, which returns a vector of as many colors than the slice has rows. It can make use of any argument described on this page (including custom arguments passed via "..."), as its enclosing environment is redefined to the calling one. colorVal must be NA for the function to be used.
border
The color to fill box borders with (as a name, an integer or an hexadecimal character description).
cex.lab
The relative character size of x and y axis labels (default: 1). See par.
spacing
Single numeric value, the vertical spacing between boxes, in proportion of the box height.
bty
A character string which determined the type of box which is drawn about plots. If bty is one of "o" (the default), "l", "7", "c", "u", or "]" the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box. See par.
groupBy
Single character value, the name of a slice column to use for feature grouping. Grouped features are drawn on the same line, and joined by an horizontal segment. Use NA to disable feature grouping.
groupPosition
Single character value, the name of an integer slice column with the position of the feature in the group (starting at 1). If groupBy is provided with groupPosition and groupSize, groups containing out-of-range elements will be extended to the screen boundary. Use NA if feature grouping is disabled, or if awareness of out-of-range features is not critical.
groupSize
Single character value, the name of an integer slice column with the total amount of features in the group. See groupPosition.
groupLwd
Single numeric value, the width of the line drawn to group elements.
…
Further arguments to be passed to draw.bg.