Description Usage Arguments Value See Also Examples
View source: R/plotIdiograms.R
This function reads a data.frame passed to dfChrSize
with columns: chrName
(mono/holo) and
shortArmSize
and longArmSize
for monocentrics or a column chrSize
for holocentrics and produces a plot of idiograms. If more
than one species, a column named OTU
is needed.
Optionally, it reads another data.frame passed to dfMarkPos
with the position of
marks (sites). Examples: markposDFs
. Another data.frame for mark characteristics
can be used dfMarkColor
or a character vector passed to mycolors
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 | plotIdiograms(
dfChrSize,
defaultFontFamily,
revOTUs = FALSE,
karHeight = 2,
karHeiSpace = 2.5,
karSepar = TRUE,
amoSepar = 10,
addMissingOTUAfter = NA,
addMissingOTUBefore = NA,
missOTUspacings = 0,
moveKarHor = "",
moveAllKarValueHor = 0,
moveAllKarValueY = 0,
karAnchorLeft = "",
karAnchorRight = "",
anchor = FALSE,
anchorLineLty = 1,
anchorText = "",
anchorTextMParental,
anchorTextMoveX = 0.5,
anchorTextMoveY = 1,
anchorTextMoveParenX = 0,
anchorTextMoveParenY = 0,
anchorVsizeF = 0.5,
anchorHsizeF = 1,
pchAnchor = 23,
moveAnchorV = 0,
moveAnchorH = 0,
mkhValue = 0.5,
n = 50,
markN = 25,
notes,
leftNotes,
leftNotesUp,
notesTextSize = 1,
leftNotesTextSize = 1,
leftNotesUpTextSize = 1,
notesLeft,
notesPosX = 0.5,
notesPosY = 0,
leftNotesPosX = 0.5,
leftNotesPosY = 0,
leftNotesUpPosX = 0.5,
leftNotesUpPosY = 0,
noteFont = 1,
leftNoteFont = 1,
leftNoteFontUp = 1,
parseTypes = TRUE,
parseStr2lang = FALSE,
propWidth = FALSE,
MbThreshold = 10000,
threshold = 35,
MbUnit = "Mb",
yTitle = "µm",
specialyTitle = "cM",
specialOTUNames = "",
addOTUName = TRUE,
OTUTextSize = 1,
OTUfont,
OTUfamily = "",
OTUasNote = FALSE,
OTUasLeftNote = FALSE,
orderChr = "size",
chrId = "original",
classMbName = "Pm.",
classcMName = "L.G.",
classChrName = "Chr.",
classChrNameUp = "Type",
classGroupName = "",
chrNameUp = FALSE,
chrIdPatternRem,
indexIdTextSize = 1,
distTextChr = 1,
groupUp = FALSE,
groupName = TRUE,
groupSepar = 0.5,
chromatids = TRUE,
arrowsBothChrt = TRUE,
holocenNotAsChromatids = FALSE,
excHoloFrArrToSide = FALSE,
xModifier = 12,
xModMonoHoloRate = 1,
chrWidth = 0.5,
chrSpacing = 0.5,
specialChrWidth = 0.3,
specialChrSpacing = 0.7,
chrColor = "gray",
chrBorderColor,
centromereSize = 0,
autoCenSize = TRUE,
cenColor,
fixCenBorder = NULL,
gishCenBorder = FALSE,
hideCenLines = 1.75,
roundedCen,
cenFormat = "rounded",
cenFactor = 1,
squareness = 4,
lwd.chr = 0.5,
lwd.cM,
lwd.marks = 99,
dfMarkPos,
defaultStyleMark = "square",
markDistType = "beg",
protruding = 0.2,
startPos = 0,
pMarkFac = 0.25,
origin = "b",
efZero = 1e-05,
cMBeginCenter = FALSE,
arrowhead = 0.3,
shrinkArrow = 0.3333,
arrowheadWidthShrink = 0.1,
arrowsToSide = TRUE,
useOneDot = FALSE,
dotsAsOval = FALSE,
dfMarkColor,
mycolors,
borderOfWhiteMarks = TRUE,
colorBorderMark = "",
lwd.mimicCen,
defCenStyleCol,
pattern = "",
legend = "aside",
remSimiMarkLeg = TRUE,
bannedMarkName,
bMarkNameAside = FALSE,
forbiddenMark,
legendWidth = 1.7,
legendHeight = NA,
markLabelSize = 1,
markLabelSpacer = 1,
legendYcoord = 0,
markNewLine = NA,
mylheight = 0.7,
chrSize = FALSE,
nsmall = 1,
chrSizeMbp = FALSE,
markPer = "",
showMarkPos = FALSE,
bToRemove = "",
perAsFraction = FALSE,
chrIndex = "both",
morpho = "both",
nameChrIndexPos = 2,
karIndex = TRUE,
karIndexPos = 0.5,
ruler = TRUE,
useMinorTicks = FALSE,
miniTickFactor = 10,
rulerPos = 0,
ruler.tck = -0.02,
rulerNumberPos = 0.5,
rulerNumberSize = 1,
collapseCen = TRUE,
rulerInterval = 0,
rulerIntervalcM = 0,
rulerIntervalMb = 0,
ceilingFactor = 0,
xPosRulerTitle = 2.6,
yPosRulerTitle = 0,
rulerTitleSize = 1,
xlimLeftMod = 1,
xlimRightMod = 2,
ylimBotMod = 0.2,
ylimTopMod = 0.2,
callPlot = TRUE,
asp = 1,
circularPlot = FALSE,
verticalPlot = TRUE,
karSpaceHor = 0,
shrinkFactor = 0.9,
separFactor = 1.5,
labelSpacing = 0.7,
labelOutwards = FALSE,
chrLabelSpacing = 0.5,
radius = 0.5,
rotation = 0.5,
circleCenter = 1,
circleCenterY = 1,
OTUlabelSpacing = 0.3,
OTUsrt = 0,
OTUplacing = "first",
OTULabelSpacerx = 0,
OTULabelSpacery = 0,
OTUcentered = TRUE,
OTUjustif = 0,
OTUlegendHeight = NA,
roundness,
...
)
|
dfChrSize |
mandatory data.frame, with columns: |
defaultFontFamily |
character. use this as the font family. No default value. |
revOTUs |
boolean, The order of species is the one in the main
data.frame, use |
karHeight |
numeric, vertical size of karyotypes. See also |
karHeiSpace |
numeric, vertical size of karyotypes including spacing. Use with |
karSepar |
boolean, reduce distance among karyotypes |
amoSepar |
numeric, depends on |
addMissingOTUAfter |
character, when you want to add space (ghost OTUs) after one or several OTUs, pass the names of OTUs preceding the desired space in a character vector i.e. |
addMissingOTUBefore |
character, when you want to add space (ghost OTUs) before one or several OTUs, pass the names of OTUs after the desired space in a character vector i.e. |
missOTUspacings |
numeric, when you use |
moveKarHor |
character, OTUs' names of karyotypes that should be moved horizontally. See |
moveAllKarValueHor |
numeric, similar to |
moveAllKarValueY |
numeric, similar to |
karAnchorLeft |
character, OTUs' add anchor to the left of this OTU names of karyotypes. For |
karAnchorRight |
character, OTUs' add anchor to the right of this OTU names of karyotypes. For |
anchor |
boolean, when |
anchorLineLty |
numeric, type of line in |
anchorText |
character, text to add to |
anchorTextMParental |
character, designed to fill with a character object the space left of a missing parental in the |
anchorTextMoveX |
numeric, for vertical plots with |
anchorTextMoveY |
numeric, for horizontal plots with |
anchorTextMoveParenX |
numeric, for plots with |
anchorTextMoveParenY |
numeric, for plots with |
anchorVsizeF |
numeric, factor to modify vertical size of anchor |
anchorHsizeF |
numeric, factor to modify horizontal size of anchor |
pchAnchor |
numeric, symbol for anchor, see |
moveAnchorV |
numeric, displace anchor vertical portion to right or left. See |
moveAnchorH |
numeric, displace anchor horizontal portion to right or left. See |
mkhValue |
numeric, value to move kar. hor. See |
n, |
numeric vertices number for round corners |
markN, |
numeric vertices number for round corners of marks |
notes, |
data.frame, or csv file name in quotes, (shown to the right of kar.), with columns |
leftNotes, |
data.frame, or csv file name in quotes (shown to the left), with columns |
leftNotesUp, |
data.frame, or csv file name in quotes, (shown to the left-up), similar to |
notesTextSize |
numeric, font size of notes, see |
leftNotesTextSize |
numeric, font size of notes, see |
leftNotesUpTextSize |
numeric, font size of notes, see |
notesLeft |
deprecated, use a data.frame for |
notesPosX |
numeric, move right notes to the right or left (x axis) |
notesPosY |
numeric, move right notes down or up (y axis) |
leftNotesPosX |
numeric, move left notes to the right or left (x axis) |
leftNotesPosY |
numeric, move left notes ( |
leftNotesUpPosX |
numeric, move up left notes to the right or left (x axis) |
leftNotesUpPosY |
numeric, move up left notes ( |
noteFont, |
numeric |
leftNoteFont, |
numeric |
leftNoteFontUp, |
numeric |
parseTypes, |
boolean, parse in |
parseStr2lang, |
bolean, parse string in |
propWidth, |
boolean, defaults to |
MbThreshold, |
numeric, if greater than this number (defaults to |
threshold, |
this is the max. value allowed for the main two significative digits, otherwise scale will shrink. For example, after 35 μ m (Default), apparent size will be 3.5 and scale interval will change. See also |
MbUnit, |
character, text of units of title when |
yTitle |
character, units for common title. Defaults to μ m |
specialyTitle, |
character, title of ruler if OTU is in |
specialOTUNames |
character vector, normally title of ruler is micrometer or Mb (big numbers). Use this param. to be able to put a different unit in ruler title. See |
addOTUName |
boolean, when |
OTUTextSize |
numeric, font size of OTU name (species). Defaults to |
OTUfont |
numeric, |
OTUfamily |
character, font family for OTU name. |
OTUasNote |
boolean, when |
OTUasLeftNote |
boolean, when |
orderChr |
character, when |
chrId |
character, print name of chromosome, |
classMbName |
character, name of "chromosome" when in Mbp. Defaults to |
classcMName |
character, name of "chromosome" when OTU in |
classChrName |
character, name of "chromosome" when in micrometers (apparently). Defaults to |
classChrNameUp |
character, name of "chromosome" for col. |
classGroupName |
character, name of groups. Defaults to |
chrNameUp |
boolean, when |
chrIdPatternRem |
character, regex pattern to remove from chr. names |
indexIdTextSize |
numeric, font size of chr. and kar. indices and
chromosome name. Defaults to |
distTextChr |
numeric, distance from name of chromosome to chromosome,
also affects vertical separation of indices. Defaults to |
groupUp |
boolean, when |
groupName |
boolean, when |
groupSepar |
numeric, factor for affecting chr. spacing |
chromatids |
boolean, when |
arrowsBothChrt |
boolean, when |
holocenNotAsChromatids |
boolean, when |
excHoloFrArrToSide |
boolean, when |
xModifier |
numeric, for |
xModMonoHoloRate |
numeric, factor to shrink chromatid separ. for holocen. 5 means 5 times smaller (quotient). |
chrWidth |
numeric, relative chromosome width. Defaults to |
chrSpacing |
numeric, horizontal spacing among chromosomes, see also |
specialChrWidth |
numeric, relative chromosome width. Defaults to |
specialChrSpacing |
numeric, horizontal spacing among chromosomes for OTUs in |
chrColor |
character, main color for chromosomes. Defaults to |
chrBorderColor |
character, color for border of chromosomes, defaults to |
centromereSize |
numeric, optional, this establishes the apparent size of cen. in the plot in μm. See |
autoCenSize |
boolean, when |
cenColor |
character, color for centromeres, if GISH use |
fixCenBorder |
boolean, when |
gishCenBorder |
boolean, when |
hideCenLines |
numeric, factor to multiply line width (lwd) used for covering cen. border, when |
roundedCen |
deprecated, see cenFormat |
cenFormat |
boolean, when |
cenFactor |
numeric, modifies any cen. mark and cen. size. Defaults to |
squareness |
numeric, shape of vertices of chromosomes and square marks,
higher values more squared. Defaults to |
lwd.chr |
thickness of border of chr., some marks and ruler. Thick of |
lwd.cM |
thickness of cM marks. Defaults to |
lwd.marks |
thickness of most marks. Except |
dfMarkPos |
data.frame of marks (sites): columns: |
defaultStyleMark |
character, default style of mark, only used when |
markDistType |
character, if |
protruding |
numeric, when style of mark is |
startPos |
numeric, factor to increase separation of |
pMarkFac |
numeric, fraction of chr. size for |
origin, |
For non-monocentric chr. (for holocentrics only) Use |
efZero, |
numeric, numbers below this one will be considered as zero, for comparison purposes. Defaults to |
cMBeginCenter, |
boolean, start position of |
arrowhead |
numeric, proportion of head of arrow (mark styles: |
shrinkArrow |
numeric, proportion, shrinks body of arrow. Defaults to |
arrowheadWidthShrink |
numeric, proportion, shrinks head of arrow. Defaults to |
arrowsToSide |
boolean, when |
useOneDot |
boolean, use one dot instead of two in style of marks |
dotsAsOval |
boolean, use oval instead of two dots in style of marks |
dfMarkColor |
data.frame, optional, specifying colors and style for marks (sites);
columns: |
mycolors |
character vector, optional, i.e. |
borderOfWhiteMarks |
boolean, if |
colorBorderMark |
character, without default, pass a name of a color to use as border of marks. See |
lwd.mimicCen |
thickness of lines of |
defCenStyleCol |
character, color of outer part of |
pattern |
REGEX pattern to remove from names of marks |
legend |
character, |
remSimiMarkLeg |
boolean, when |
bannedMarkName |
character, character string or vector with mark names to be removed from plot. Not the marks but the labels. Except when |
bMarkNameAside |
boolean, when |
forbiddenMark, |
character, character string or vector with mark names to be removed from plot. Not the marks but the labels. |
legendWidth |
numeric, factor to increase width of squares and of legend. Defaults to |
legendHeight |
numeric, factor to increase height of squares and dots of legend. Automatic. |
markLabelSize |
numeric, only if legend != (not) "", size of the font of
labels of marks (legend). Defaults to |
markLabelSpacer |
numeric, only if |
legendYcoord |
numeric, modify Y position of legend when |
markNewLine, |
character, character to split mark Names into different lines. Applies to |
mylheight, |
numeric, for |
chrSize |
boolean, when |
nsmall |
numeric, rounding decimals for |
chrSizeMbp |
boolean, when |
markPer |
character vector, name of mark(s) to calculate % of mark in chr. and add it to plot. See |
showMarkPos |
boolean, adds position of marks under karyotype (fraction 0-1) when |
bToRemove, |
character vector, bands to remove from calc. of pos., when |
perAsFraction |
boolean, when |
chrIndex |
character, add arm ratio with |
morpho |
character, when |
nameChrIndexPos |
numeric, modify position of name of chr. indices |
karIndex |
logical, add karyotype indices A (intrachromosomal - centromere pos.) and A2 (interchromosomal asymmetry, variation among chromosome sizes) |
karIndexPos |
numeric, move karyotype index. Defaults to |
ruler |
boolean, display ruler to the left of karyotype, when |
useMinorTicks |
boolean, display minor ticks between labeled ticks in ruler. See |
miniTickFactor |
numeric, number of minor ticks for each labeled tick. See |
rulerPos |
numeric, absolute position of ruler, corresponds to |
ruler.tck |
numeric, tick size of ruler, corresponds to |
rulerNumberPos |
numeric, modify position of numbers of ruler. Defaults to |
rulerNumberSize |
numeric, size of number's font in ruler. Defaults to |
collapseCen |
boolean, avoid spacing in ruler between short arm and long arm. |
rulerInterval |
numeric, intervals in ruler. No default, automatic. |
rulerIntervalcM |
numeric, intervals in ruler of OTU in |
rulerIntervalMb |
numeric, intervals in ruler of OTU with data in Mb (> |
ceilingFactor |
numeric, affects number of decimals for ceiling. Affects max. value of ruler. Defaults to |
xPosRulerTitle, |
numeric, modify position of ruler title. See |
yPosRulerTitle, |
numeric, affects vertical position of ruler title. Defaults to |
rulerTitleSize, |
numeric font size of units of ruler. See also |
xlimLeftMod |
numeric, modifies |
xlimRightMod |
numeric, |
ylimBotMod |
numeric, modify |
ylimTopMod |
numeric, modify |
callPlot |
boolean, create new plot in your device. Defaults to |
asp, |
numeric, y x aspect of plot. Defaults to |
circularPlot |
boolean, if |
verticalPlot |
boolean, when |
karSpaceHor |
numeric, separation among horizontal karyotypes. When |
shrinkFactor |
numeric, for |
separFactor |
numeric, for |
labelSpacing |
numeric, for |
labelOutwards |
boolean, inline labels projected outwards |
chrLabelSpacing |
numeric, for |
radius |
numeric, for |
rotation |
numeric, anti-clockwise rotation, defaults to |
circleCenter |
numeric, for |
circleCenterY |
numeric, for |
OTUlabelSpacing |
numeric, for |
OTUsrt |
numeric, for |
OTUplacing |
character, for |
OTULabelSpacerx |
numeric, for |
OTULabelSpacery |
numeric, for |
OTUcentered |
boolean, for |
OTUjustif |
numeric, for |
OTUlegendHeight |
numeric, for |
roundness |
deprecated, use |
... |
accepts other arguments for the plot, see, |
plot
1 2 3 4 | data(dfOfChrSize)
plotIdiograms(dfOfChrSize, ylimBotMod = .75, rulerPos=-.5)
plotIdiograms(dfOfChrSize, circularPlot = TRUE, chrLabelSpacing = 1)
plotIdiograms(dfChrSizeHolo, rulerPos=-.5)
|
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