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idiogramFISH: Shiny App. Idiograms with Marks and Karyotype Indices

News

idiogramFISH 2.0.13

22-08-2023

Docs:

  • Fix arguments descriptions

idiogramFISH 2.0.12

06-06-2023

Docs:

  • Fix link on DESCRIPTION file

idiogramFISH 2.0.11

05-04-2023

Bug:

  • Fix genBank processing when only one match

idiogramFISH 2.0.10

05-04-2023

param:

  • alpha_val: modify transparency of marks

idiogramFISH 2.0.9

14-09-2022

  • refactoring of code

idiogramFISH 2.0.8

27-12-2021

  • Accepts .csv files to notes parameters
  • circularPlot=TRUE now compatible with chromatids=TRUE showing chromatids in circ. plots
  • centromere is now subtracted from arm, so ruler is continuous in monocen. (collapseCen).
  • new chrRegion possible (column in data.frame dfMarkPos): pcen qcen. It’s behavior is similar to cen

param:

  • dfCenMarks: deprecated
  • collapseCen: boolean, avoid spacing in ruler between short arm and long arm.
  • anchorHsizeF: numeric, factor to modify horizontal size of anchor 1 (default).

Shiny:

  • Change in default values for new data.frames
  • Fixed parsing of yTitle in code tab
  • Download and upload custom presets

idiogramFISH 2.0.6

27-09-2021

  • Added possibility of showing several % (span) of marks, ex. markPer = c("5S","45S")
  • perMark and posCalc functions produce data.frames
  • Added parameters: autoCenSize, leftNotesUpPosX
  • Modified parameters: centromereSize, rulerIntervalMb
  • function asymmetry better dealing with unexpected cases
  • function armRatioCI better dealing with unexpected cases

Shiny:

  • New menu stats to export indices and marks’ stats
  • Several parameters added
  • Several examples added to presets

Bugs:

  • Better dealing with horizontal karyotypes
  • Fixed bug of displaying pos. of bands when showMarkPos= TRUE

param:

  • rulerIntervalMb: Use data in millions
  • leftNotesUpPosX: numeric, move up left notes to the right or left (x axis)
  • autoCenSize boolean, when TRUE ignores centromereSize
  • centromereSize: Apparent size of centromeres. Requires autoCenSize = FALSE
  • showBandList in posCalc function to avoid adding mark names

idiogramFISH 2.0.5

19-05-2021

Shiny:

  • New dependence install options for the shiny app runBoard() function
  • Better dealing with pandoc versions in shiny app

idiogramFISH 2.0.4

23-04-2021

  • Fixed bug of too many fonts (angles) when hundreds of marks for .svg for labelOutwards=TRUE
  • jupyter notebooks for working locally or online in colab

Shiny:

idiogramFISH 2.0.3

12-04-2021

  • Improvements in genBankReadIF function

Shiny:

  • Downloading with rentrez package and plotting of chromosomes in shiny app

param:

  • markN numeric, vertices number for round corners of marks

idiogramFISH 2.0.2

02-03-2021

  • Added new style of mark exProtein (param: startPos, pMarkFac) and inProtein for circular plots also.
  • Added new style of centromere inProtein
  • better reading of genBank data by function genBankReadIF
  • changes in dealing with chrWidth and other param. in circular plots
  • Added parameters: startPos, pMarkFac,cenFormat,cenFactor
  • Modified parameters: bannedMarkNameAside, xModifier, roundedCen

param:

  • bannedMarkNameAside renamed to bMarkNameAside
  • startPos numeric, factor to increase separation of exProtein marks to chromosome. Defaults to 0
  • pMarkFac numeric, fraction of chr. size for exProtein style marks. Defaults to 0.25
  • xModifier was modified, now quotient of chrWidth
  • roundedCen: deprecated, see cenFormat
  • cenFormat: character, when "triangle", cen. has triangular aspect. When "rounded", it has rounded aspect (Default). "inProtein" for using the mark with style of same name.
  • cenFactor: numeric, modifies any cen. mark and cen. size. Defaults to 1

Shiny App:

  • Several changes in UI
  • show/hide default values in code tab
  • save data.frames as .rds too
  • better update of log tab

idiogramFISH 2.0.0

05-02-2021

  • Added option to add OTU name as leftNotesUp (OTUasLeftNote)

Shiny:

param:

  • anchorTextMoveParenX numeric, for plots with anchorTextMParental move text in X axis. Defaults to 0
  • anchorTextMoveParenY numeric, for plots with anchorTextMParental move text in Y axis. Defaults to 0
  • OTUasLeftNote boolean, when TRUE adds OTU (species) name to the left-up

idiogramFISH 1.16.8

30-11-2020

  • Added rounded vertices for ggplot related functions
  • Better parsing of FL (chr. name formatting) and similar text in notes
  • Sorting of chr. by chrNameUp column added.

param:

  • leftNotesUpPosY numeric, move up-left-notes leftNotesUp down or up (y axis)

idiogramFISH 1.16.7

15-10-2020

  • Helper functions for simple plots with ggplot mapGGChr and mapGGChrMark
  • Better customization of anchor

param:

  • 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. c("species one","species five")
  • karAnchorRight: character, OTUs’ add anchor to the right of this OTU (names of karyotypes). For verticalPlot=FALSE
  • anchorText: character, text to add to anchor structure near symbol. See anchor. Defaults to ""
  • anchorTextMParental: character, designed to fill with a character object the space left of a missing parental in the anchor structure.
  • anchorTextMoveX: numeric, for vertical plots with anchorText move text in X axis. Defaults to 0.5
  • anchorTextMoveY: numeric, for horizontal plots with anchorText move text in Y axis. Defaults to 1
  • anchorLineLty: numeric, type of line in anchor, corresponds to lty. Defaults to 1

idiogramFISH 1.16.6

16-09-2020

  • Support for F+ chr. types in citrus functions
  • Horizontal arrange introduced verticalPlot=FALSE
  • Horizontal anchor for karyotypes in karAnchorLeft
  • Move all karyotypes moveAllKarValueY, moveAllKarValueHor
  • Introducing more notes, over kar., leftNotesUp
  • dotsAsOval convert dots style to one oval. not for circ. plots.
  • useOneDot now for regular plots (non-circular) also.
  • better plotting of white chr. in circular plots
  • Fixed bug of dots size in circular plots
  • Fixed bug of ruler of long arm.
  • Fixed bug when chr. name FL
  • Fixed bug when calculating mark size when NA - GISH
  • Better plotting of white chr.
  • square marks name splitting

param:

  • verticalPlot: boolean, when TRUE karyotypes are plotted vertically, otherwise, horizontally. Defaults to TRUE
  • karSpaceHor: numeric, separation among horizontal karyotypes. When verticalPlot=FALSE. Defaults to 0
  • karAnchorLeft: character, OTUs’ names of karyotypes to the right of your desired anchor. For verticalPlot=FALSE
  • moveAllKarValueHor: numeric, similar to mkhValue, but affects all karyotypes.
  • moveAllKarValueY: numeric, similar to moveAllKarValueHor, but affects y axis.
  • leftNotesUp: data.frame, (to the left), similar to leftNotes, but intended for placement over kar.
  • leftNotesPosX: (0.5) numeric, moves left notes in the x axis
  • notesPosX: (0.5) numeric, moves right notes in the x axis
  • noteFont: numeric 1 for normal, 2 for bold, 3 for italics, 4 for bold-italics. See notes
  • leftNoteFont: numeric 1 for normal, 2 for bold, 3 for italics, 4 for bold-italics. See leftNotes
  • leftNoteFontUp: numeric 1 for normal, 2 for bold, 3 for italics, 4 for bold-italics. See leftNotesUp
  • parseTypes: boolean, parse in notes the Citrus chr. types names. Creates subindex pos. for FL.
  • parseStr2lang: bolean, parse string in notes with function str2lang(paste0("paste(",note,")") ) for ex: "italic('C. sinensis'), ' Author'". See notes, leftNotes,leftNotesUp.
  • gishCenBorder: boolean, when TRUE, cen. mark border color is the same as mark color, ignoring colorBorderMark. No default.
  • hideCenLines: numeric, factor to multiply line width (lwd) used for covering cen. border, when chrColor is white or when gishCenBorder=TRUE
  • markNewLine, character, character to split mark Names into different text lines. Applies to square marks. Defaults to NA
  • mylheight, numeric, for markNewLine!=NA; is equivalent to lheight of par: “The line height multiplier. The height of a line of text (used to vertically space multi-line text) is found by multiplying the character height both by the current character expansion and by the line height multiplier.” Defaults to 0.7.
  • bMarkNameAside: boolean, when TRUE and legend="inline", shows marks in bannedMarkName as legend="aside" would do. See bannedMarkName
  • forbiddenMark: character, character string or vector with mark names to be removed from plot. Not the marks but the labels.
  • lwd.marks: thickness of most marks. Except cM marks and centr. related marks. See lwd.chr, lwd.cM
  • dotsAsOval: boolean, use oval instead of two dots in style of marks dots. Defaults to FALSE. See useOneDot. Not useful for chromatids=TRUE or circularPlot=TRUE

idiogramFISH 1.16.1

29-07-2020

  • squareLeft new style of mark. as square but with legend to the left when inline.
  • minor ticks possible
  • add mark % of chr. and position to plot.
  • additional column chrNameUp for name over kar.
  • show chr. sizes in μm and Mbp under kar.
  • when OTUfont=3 (italics), var. name present inside ' is not shown in italics
  • added anchor structure for progenies, see GISH
  • notesLeft deprecated pass data.frame to leftNotes
  • Better separation of groups
  • FL+ chr. name now corrected in plot, previously FLNA
  • ylabline renamed to xPosRulerTitle

param:

  • groupSepar: numeric, factor for affecting chr. spacing chrSpacing among groups. Defaults to 0.5
  • useMinorTicks: boolean, display minor ticks between labeled ticks in ruler. See miniTickFactor. Defaults to FALSE. (ticks without label)
  • miniTickFactor: numeric, number of minor ticks for each labeled tick. See useMinorTicks. Defaults to 10
  • xPosRulerTitle: (2.6) Modifies the horizontal position of the title of rulers (Mb, etc). Moves to left from 1st chr. in chrSpacing times
  • yPosRulerTitle: numeric, affects vertical position of ruler title. Defaults to 0
  • markPer: character, name of mark to calculate % of mark in chr. and add it to plot. See perAsFraction
  • perAsFraction: boolean, when TRUE % is shown as fraction. Defaults to FALSE. See markPer
  • showMarkPos: boolean, adds position of marks under karyotype (fraction 0-1) when TRUE. Defaults to FALSE
  • bToRemove: character, bands to remove from calc. of pos.
  • chrSize show chr. size under karyo.
  • chrNameUp use col. of the same name to add secondary name over kar.
  • classMbName “chromosome” name when in Mbp
  • classcMName “chromosome” name when in cM
  • classChrName “chromosome” name when in μm
  • classChrNameUp “chromosome” name chrNameUp
  • classGroupName name of title of groups
  • nsmall digits for rounding of chrSize
  • chrSizeMbp show chr. size Mbp requires col. Mbp
  • groupName, hide or show group name
  • leftNotes, similar to notes
  • leftNotesPosX, x
  • leftNotesPosY, y
  • moveKarHor, move kar. to right
  • mkhValue, amount to move to right
  • anchor, display anchor for moveKarHor OTUs
  • anchorVsizeF factor to modify vertical size of anchor
  • moveAnchorV, move anchor vertical portion
  • moveAnchorH, move anchor horizontal portion
  • pchAnchor, symbol in anchor
  • rulerPosMod deprecated

idiogramFISH 1.15.3

01-07-2020

main changes:

  • Better plotting of GISH with chromatids
  • change in messages when missing data
  • chr. in groups are closer
  • parsing of citrus names of chromosomes FL+ and FL0 automatic
  • helper functions for plotting Citrus karyotypes:
    • citrusSize, citrusMarkPos, markOverCMA

param: (plotIdiograms)

  • efZero threshold for checking if != 0
  • orderChr, order of chr. Replaces orderBySize - deprecated. Values = size, original, name, group
  • orderBySize - deprecated
  • notesLeft note position to the left when TRUE
  • notesPosY y axis modify notes position
  • chrIdPatternRem regex pattern to remove from chr. names

idiogramFISH 1.15.1

02-06-2020

  • introducing ‘chromatids’
  • new rounded style of centromere added (default).
  • better naming of w position marks when inline
  • changed logic of cenStyle coloring

param:

  • chromatids show separated chromatids
  • holocenNotAsChromatids do not use chromatids in holocen.
  • arrowsBothChrt prints arrow marks in both chromatids
  • excHoloFrArrToSide excludes holocentrics from arrowsToSide config.
  • xModifier separation among chromatids
  • xModMonoHoloRate shrink holocen. separ among chromatids with this quotient.
  • remSimiMarkLeg remove “duplicated” name of labels when presence of pseudoduplicates arising from pattern
  • bannedMarkName remove this mark name from labels (legends)
  • defCenStyleCol color for external part of marks with cenStyle
  • roundedCen rounded centromere
  • lwd.mimicCen line width for cenStyle marks
  • squareness new name for roundness (deprecated)

idiogramFISH 1.14.11

23-04-2020

  • genBankReadIF function, now allows duplicated field names
  • cMLeft style of mark added
  • cM and cMLeftstyles are used as inline type of legend for arrows (upArrow,downArrow)
  • A new column protruding can be added to dfMarkColor data.frame to define aspect of cM marks
  • namesToColumns new function to avoid overlap of mark names, for holoc. and monoc.

params (namesToColumns):

  • marksDf data.frame of marks
  • dfChrSize data.frame, size of chr. same as plot.
  • markType of type “downArrow”,“upArrow”,“cM”,“cMLeft”
  • amountofSpaces numeric, number of spaces for each column
  • colNumber numeric, number of columns
  • protruding numeric, same as plot, equivalent to cM protruding
  • protrudingInt numeric, spacing of columns in terms of width of chr. percent 1 = 100%.
  • circularPlot same as plot
  • rotation same as plot
  • defaultStyleMark if some data in column style missing fill with this one
  • orderBySize same as in plot.
  • halfModUp when plotting several chromosomes in a circular plot, corrects for alignment problems of “upArrows”, “cM” labels.
  • halfModDown when plotting several chromosomes in a circular plot, corrects for alignment problems of “downArrows”, “cMLeft” labels.
  • rotatMod for circ. plots, when rotation diff. from 0, corrects alignment of labels.

params:

  • cMBeginCenter modifies start position of cM and cMLeft marks
  • arrowsToSide arrows are plotted near chr. margin

idiogramFISH 1.14.7

27-03-2020

  • Compatibility with rentrez downloaded data
  • Better reading of join from genBank data
  • new styles of mark: cenStyle to add constrictions anywhere; upArrow (clockwise in circular plot); downArrow (anti-clockwise in circular plot)
  • fixed bug when legend="inline" in circular plots

params:

  • rulerTitleSize: Font size of units (title)
  • arrowhead: proportion of head of arrow - length
  • shrinkArrow: proportion to shrink body of arrow - width
  • arrowheadWidthShrink: proportion to shrink arrowhead - width

idiogramFISH 1.14.2

26-02-2020

  • Introducing circular plots circularPlot=TRUE and other params. for circular plot
  • function genBankReadIF to read plasmid or prokaryote data. Uses tidyr.
  • function swapChrRegionDfSizeAndMarks to swap arm size and marks
  • tolerance when column markSize absent

params:

  • legendYcoord: modify mark legend Y pos (for common plot also)
  • callPlot: call plot.new or use your device (when FALSE)

params: (circularPlot=TRUE)

  • shrinkFactor: size of chr. in fraction of circle
  • separFactor: separ among kar.
  • labelSpacing: among label and chr.
  • chrLabelSpacing: chr. label space
  • OTUlabelSpacing: OTU name space
  • radius: radius
  • OTUsrt: angle of OTU name text
  • OTUplacing: add number and legend instead of OTU name
  • useOneDot: one dot instead of two
  • circleCenter: X coordinate
  • circleCenterY: Y coordinate
  • OTULabelSpacerx: modify OTU name pos.
  • OTULabelSpacery: modify OTU name pos.
  • OTUcentered: OTU name centered
  • OTUjustif: OTU name justif.
  • OTUlegendHeight: separ. of OTU names when OTUplacing

idiogramFISH 1.13.8

05-02-2020

  • Fixed bug when plotting several OTU with groups
  • cen. marks allowed also when centromereSize = 0
  • improvement in automatic scale of ruler.
  • Added the “cM” style of mark, with custom protruding
  • centromereSize is automatic (when absent), as well as rulerInterval

params:

  • lwd.cM: thickness of cM marks
  • OTUfont: style of font of OTU name
  • OTUfamily: font family for OTU names
  • lwd.chr: affects ruler too.
  • defaultFontFamily: modify font of texts.
  • Custom default style of mark with defaultStyleMark
  • fixCenBorder affects cen. marks also.
  • chrBorderColor for adding optionally chr. border color.
  • cenColor defaults to chrColor now.
  • colorBorderMark forces custom color in border of marks.
  • borderOfWhiteMarks, if TRUE, when mark is white, its border is black.
  • ceilingFactor number of significative digits to consider when rounding ruler max. value.
  • MbThreshold created (substitutes MbThresholds)
  • added option to modify ruler intervals for Mb, and cM independently with params: rulerIntervalMb, rulerIntervalcM
  • other added parameters: defaultStyleMark, protruding, ceilingFactor, rulerInterval, threshold, MbUnit, specialChrWidth, specialChrSpacing, specialOTUNames, specialyTitle
  • OTUs passed to specialOTUNames, can have special: specialChrWidth, specialChrSpacing, and specialyTitle. Useful for e.g. cM.
  • Allowed customization of ruler (ceilingFactor, rulerInterval)
  • Allowed custom ruler title MbUnit, specialyTitle, yTitle. yTitle is the common (micrometers). specialyTitle is for OTUs in specialOTUNames (e.g. “cM”), and MbUnit when data in millions and OTU is not in specialOTUNames

idiogramFISH 1.12.1

06-01-2020

  • Fixed bug of absence of chr. indices when monocen. and holocen. together
  • Added functionality to print each index separately
  • Added functionality to print groups below chr. name
  • DOI added
  • minor vignette corrections

idiogramFISH 1.11.1

12 12 2019

  • Added functionality for fixing y x aspect ratio (roundness proportion) using asp = 1 only
  • Use of dotRoundCorr discouraged, requires useXYfactor = TRUE
  • Fixed misplacement of marks when origin="t" or markDistType = "cen"
  • Added functionality for plotting karyotypes in micrometers and bases together, see monocen. vignette

idiogramFISH 1.9.1

29 11 2019

  • Fixed bug when centromere=0 when several karyotypes
  • Added rounded vertices for centromere > 0
  • Added functionality for plotting GISH.

idiogramFISH 1.8.3

14 11 2019

  • Fixed dependencies
  • Fixed size of dots of legend

idiogramFISH 1.8.1

29 10 2019

  • Added parameters for adding notes to the right of karyotype.
  • Improvement in messages when plotting.

idiogramFISH 1.7.1

20 10 2019

  • Cen. marks don’t need another data.frame. Can be present in main marks data.frame
  • Allowed dup. names for not ordered chr. names (and no marks)

idiogramFISH 1.6.3

13 10 2019

  • More tolerance when allowing duplicated chr. names when no marks.
  • Documentation changes, new examples.

idiogramFISH 1.6.1

02 10 2019

  • Added support to plot monocen. and holocen. together
  • Function plotIdiogramsHolo deprecated

idiogramFISH 1.5.1

27 09 2019

  • Added support to plot alongside phylogenies
  • Allow some karyotypes to appear without indexes when error in long / short classif.
  • Fixed bug in naming of OTUs.
  • Vignettes corrections
  • Fix references of packages in vignettes when package not installed.
  • Added support for vignettes in devel. in R-32 bits

idiogramFISH 1.2.1

17 09 2019

  • Fixed bug in armRatioCI that impacts all other functions.
  • Added support for groups
  • Added human karyotype
  • Added rounded vertices when centromereSize =0
  • You don’t have to use dfMarkColor data.frame, is not mandatory now.
  • You can use (optionally) a character vector to pass colors.
  • Package has default colors now.

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