"shadingColors" arguments are "blues", "reds", "standard area", and "accessible area" (see documentation of "functional", valid shadingModeArg arguments are Shading mode currently the shading modesīe a single numeric threshold between 0 and 100 or two thresholdsīetween 0 and 100 in increasing order. Horizontal and 0.3in for the vertical margin. Vertical margins, respectively the default is 0.1in for the Possibilities of the customizations of the msaPrettyPrintĭocument defaults to 11in x 8.5in (US letter in landscapeĪ numeric vector of length 2 with the horizontal and This option should only be usedīy expert users and for special applciations in which the Instead, allĬustomizations must be done as LaTeX commands provided by the That customize the appearance of the output. This argument can be used to specify the entire LaTeX code If askForOverwrite is set to FALSE,įiles are overwritten without further notice.Ĭode that includes the LaTeX package times.sty if FALSE,Ĭode based on the standard LaTeX fonts (default). ![]() MsaPrettyPrint asks whether existing files should be Object provided as argument x along with the suffix The name of this file can beĭetermined with the alFile argument. MsaPrettyPrint first writes the multiple alignment x Invalid file names if not the name of an object, but an R expression Which depends on the type of output specified with the output Object provided as argument x along with the proper suffix Is given, the name of the output file defaults to name of the Multiple alignment x if not all sequences should be printed. ![]() Type of output to be generated (see details below)Ĭan be used to specify a subset of sequences in the The entire multiple alignment is printed. Which includes the classes MsaAAMultipleAlignment,Īrgument for restricting the output to a subset of columns Ĭan be a numeric vector of length 2 with a lower and an upper bound MsaPrettyPrint ( x, y, output = c ( "pdf", "tex", "dvi", "asis" ), subset = NULL, file = NULL, alFile = NULL, askForOverwrite = TRUE, psFonts = FALSE, code = NA, paperWidth = 11, paperHeight = 8.5, margins = c ( 0.1, 0.3 ), shadingMode = c ( "identical", "similar", "functional" ), shadingModeArg = NA, shadingColors = c ( "blues", "reds", "greens", "grays", "black" ), showConsensus = c ( "bottom", "top", "none" ), consensusColors = c ( "ColdHot", "HotCold", "BlueRed", "RedBlue", "GreenRed", "RedGreen", "Gray" ), consensusThreshold = 50, showLogo = c ( "top", "bottom", "none" ), logoColors = c ( "chemical", "rasmol", "hydropathy", "structure", "standard area", "accessible area" ), showLogoScale = c ( "none", "leftright", "left", "right" ), showNames = c ( "left", "right", "none" ), showNumbering = c ( "right", "left", "none" ), showLegend = TRUE, furtherCode = NA, verbose = FALSE )
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