craigw@aecom.YU.EDU (Craig Werner) (06/29/88)
.nf Measurement: inch - converts from inches to points (usually used in combination) Example: 4.25 inch 5.5 inch CENTER cm - converts from centimeters to points degree - optional (for readability) point - optional (for readability) General Definition: DEFINE - synonym of PostScript's "def" Usage: /Variable-name value DEFINE Example: /Site 2545 DEFINE percentBLACK -sets grayscale for filled segments Usage: value [0-100] percentBLACK Example: 20 percentBLACK ZEROPOINT - determines which base position is at "12:00" Usage: site [bp] ZEROPOINT Example: 396 ZEROPOINT PLASMIDLENGTH - total length of plasmid (for scaling maps to 360 degrees) Usage: length [bp] PLASMIDLENGTH Example: 2868 PLASMIDLENGTH PHAGELENGTH - synonym of PLASMIDLENGTH WIDTH -specifies the half width of a segment (dr) ticLENGTH -specifes distance from center of segment to end of tic (dR) textDISTANCE -specifies distance from center of segment to label text (dT) textLENGTH - synonym of textDISTANCE spanDISTANCE -distance of span line from main map (dS) POINTSIZE -Specifies the Point Size for text (PS) but DOES NOT reset font. SETFONT -Specifies the font, and resets typeface. ----------------------------------------------------------------------------- Circular Map Defintion: RADIUS -specifies the radius of the map (R) CENTER -specifies center of the map (X,Y) Usage: X-position Y-position CENTER Example: 4.25 inch 5.5 inch CENTER XCENTER -specifies X coordinate of map center (X) YCENTER -specifies Y coordinate of map center (Y) extLENGTH -length of an extension for extRESITE (dE) extARC -absolute angle (degrees, not bp) of the extension (aE) EXTENSION -sets both extLENGTH and extARC Circular Map Drawing Routines: arcSEGMENT -draws a circular map segment Usage: site-1 [bp] site-2 [bp] arcSEGMENT Example: 2120 3050 arcSEGMENT Notes: modified by WIDTH, percentBLACK, ZEROPOINT, among others will go across 0, i.e. 3050 120 arcSEGMENT will work arcTIC -draws a tic at a site Usage: site [bp] arcTIC Example: 0 arcTIC arcTICi -same as arcTIC, only inside the arc arcLABEL -puts a label centered on a site Usage (Text) site arcLABEL Example: (ORI) 800 arcLABEL arcRESITE -draws a tic and labels it at specified site Example: (EcoRI) 396 arcRESITE arcARROWc -draws a clockwise arrow from specified site with given length Usage: site [bp] length [bp] arcARROWc Example: 1500 100 arcARROWc Note: For promoter symbol, combine it with arcTIC arcARROWci -clockwise arrow, inside the circle arcARROWcc -counterclockwise arrow arcARROWcci -counterclockwise arrow inside the circle WEDGE extension exttic extREsite Don't ask: CenterPText -Centers Text on a point Usage: (text) xpoint ypoint CenterPText Example (pUC18) X Y CenterPText % X,Y are map center. ---------------------------------------------------------------------------- Linear Maps Definition: percentBLACK YPOSITION - sets vertical position on which linear map is centered LEFTMARGIN - sets left margin Note: LEFTMARGIN actually sets the horizontal position of the ZeroPoint (ZEROPOINT). Hence setting the left margin to the middle of the page will allow one to center diagrams on a particular restriction site. This is particularly nice for maps of nested deletions. To make it work correctly however. The PLASMIDLENGTH should not be changed for the deletions, as this will cause scaling of the base pairs. RIGHTMARGIN - set right margin Note: Actually is position of the base defined as PLASMIDLENGTH. Similar tricks can be played. WIDTH -- thickness of segment ticLENGTH -- distance from center of segment of end of tic textLENGTH -- distance from center of segment to text spanLENGTH -- distance from center of segment to span line ZEROPOINT -- the base which is aligned with the left margin PLASMIDLENGTH -- in base pairs PHAGELENGTH -- PLASMIDLENGTH and PHAGELENGTH are interchangable POINTSIZE -- a POINTSIZE and SETFONT are usually used together SETFONT >> in fact POINTSIZE only changes with SETFONT Linear Map Routines: linSEGMENT -- draws a DNA segment Usage: position1 position2 linSEGMENT Example: 0 1134 linSEGMENT linTIC -- a vertical line above segment to mark a position linTICd -- same, only below (down) the segment linLABEL -- places text above a position linLABELd -- same, only below Example: (Promoter) 100 linLABELd linCLABEL -- a label above segment centered between two sites linCLABELd -- a label below segment linRESITEh -- for restriction enzyme sites, places a tic and label linRESITEhd -- " horizontal below linRESITEv -- " vertical above linRESITEvd -- " vertical below Example: (HindIII) 450 linRESITEh linARROWr -- draws a rightward arrow (a tic length above segment) linARROWl -- leftward arrow linARROWrd -- rightward arrow below segment linARROWld -- leftward arrow below segment Usage: start length linARROW* Note: the standard promoter notation can be drawn by combining a TIC with the appropriate ARROW. Example: 1500 300 linARROW 1500 linTIC (Direction of Transcription) linLABELd linSPAN -- draws a spanning line spanLENGTH above a segment linSPANd -- draws a spanning line below segment Usage: start finish linSPAN* Note: modified by spanDISTANCE, which can be positive or negative, which makes linSPANd slighly superfluous. linNSPAN -- a spanning line with its length [bp] above it. linNSPANd -- a spanning line with its length below it. Note 1: The length is computed by the program, usage is same as linSPAN Note 2: The d (for down) refers to the position of the label with regards to the span line, not the span line in relation to the mapped SEGMENT. linLSPAN -- a spanning line with a label above it linLSPANd -- a spanning line with a label below it Usage: (text) start finish linLSPAN* These can be combined, as in: Example: 235 1000 linNSPAN (deleted in pCW16) 235 1000 linLSPANd % the net effect is the length above the span line and the comment below - note the 'd'. -- --------- Craig Werner (Lognames: werner, craigw) "This is no social crisis, just another tricky day for you."