helper function for showPhylo that does all the work
showPhylo_backend( speciesNames, nameType, dateTree = TRUE, labelType = "b", labelOffset = 0.45, aspectRatio = 1, pic = "wiki", dotsConnectText = FALSE, picSize = 1, picSaveDir, optPicWidth = 200, picBorderWidth = 10, picBorderCol = "#363636", openDir = FALSE, xAxisPad = 0.2, xTitlePad = 20, numXlabs = 8, textScalar = 1, xTitleScalar = 1, phyloThickness = 1.2, phyloCol = "#363636", textCol = "#363636", plotMar = c(t = 0.02, r = 0.5, b = 0.02, l = 0.02), clearCache = FALSE, datelifePartialMatch = TRUE, quiet = TRUE, silent = FALSE, ... )
| speciesNames | a name or vector of common or scientific names of organisms of interest (in quotes) |
|---|---|
| nameType | what type of name are you supplying? Either "sci" or "common" |
| dateTree | try to scale the tree to estimated divergence times? Uses |
| labelType | which names to label tree "leaves"? Options= "s" for scientific, "c" for common, and "b" for both (default="b") |
| labelOffset | how far from the tree tips do you want to put labels? default=0.3 (in proportion of x-axis units) |
| aspectRatio | doesn't actually work yet; the output phylogeny is always square for the moment |
| pic | what type of species image do you want to plot? options="wiki" (Wikipedia page profile image), "phylopic" (species' silhouette from the PhyloPic repository), "cust" (custom images: must be named .jpg or .png with names matching speciesNames in the picSaveDir folder), or "none" |
| dotsConnectText | do you want a dotted line to go from the text to the labels? default=FALSE |
| picSize | how big to scale images, where 1=100%; .5=50%; default=1 |
| picSaveDir | location for saving downloaded images; default=fs::path(tempdir(),"showPhylo") |
| optPicWidth | picture width in pixels for optimized versions of images saved if using pic="cust"; default= 200 |
| picBorderWidth | for pic="wiki" or "cust," what size border would you like around your image (as a %); default=10 |
| picBorderCol | color of image border; default="# 363636" (a dark, near-black color) |
| openDir | for pic="wiki" or "cust," do you want to open the picSaveDir after processing files? default=FALSE |
| xAxisPad | spacing between the phylogeny and the x-axis (scale is 1 is the distance between two sister taxa); default=.2 |
| xTitlePad | spacing between x-axis title and x numbers; default=20 |
| numXlabs | the number of year markers on the x-axis; default=8 |
| textScalar | multiplier of text size for labels and axis numbers; default=1 |
| xTitleScalar | multiplier of x-axis title size; default=1 |
| phyloThickness | how thick to make the phylogeny lines; default=1.2 |
| phyloCol | color of the phylogeny lines; default= "# 363636" |
| textCol | color of the axis and tip labels; default= "# 363636" |
| plotMar | margins around the plot area in proportional screen width units; note the right margin is much wider to make room for tip labels; default=c(t=.02,r=.4,b=.02,l=.02) for top, right, bottom, left |
| clearCache | delete cached images and taxonomic names? Passed to getPhyloNames, getWikiPics, and also applies to optimized custom images; default=FALSE |
| datelifePartialMatch | use use source trees even if they only match some of the desired taxa; affects the |
| quiet | suppress verbose feedback from the taxize package? Passed to getPhyloNames and get WikiPic helper functions. Default=TRUE |
| silent | suppress all console output? (Mainly for R documentation); Default=FALSE |
| ... | pass other parameters to |