I am trying to produce a static map via the leaflet package so I can knit it to a PDF using markdown but the circle markers on the map keep getting cut off and I can't for the life of me figure out why.
Here is the code I used to generate the map in markdown:
{r leaflet, echo=FALSE,fig.align = 'center',message=FALSE}
site=c(1,4,5,7,6,9,10,11,12,13,14,16,17,18,19,20,21,22,23,25,26,27,28,30,31,32,33,34,35,38,39,40,42,43,44,46,47,48,50,51,52,53,54,56,55,57,58,59,60,61,62,63,64,65,66,69,70,71,72,73,75,76,74,77,78,79,82,83,84,85,86,87,88,89,90,91,92,93,94,96,95,97,98,99,100,101,102,105,106,107,108,109,110,112,113,114,115,116,117,119,120,122,123,121,124,125,126,126,128,129,131,132,133,135,136,137,138,139,141,140,142,143,144,145,146,147,148,149,150,151,152,156,159,160,161,162,163,164,165,166,168,169,170,172,173,171,174,175,177,178,180,181,182,184,185,186,187,189,190,192,193,194,196,197,198,201,200,202,203,204,206,209,210,211,212,213,214,215,216,217,218,219,220,221,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,240)
lat=c(43.66184,44.79494,45.10964,43.69858,43.70498,44.62863,43.47742,43.47189,43.4778,46.1,45.32731,43.70013,44.98749,45.16991,45.36598,45.05,43.46897,43.73095,45.14393,45.08514,45.34322,44.24378,43.83065,43.67648,43.408,43.39672,45.33459,44.98288,44.95615,44.65252,43.67452,43.73467,45.14016,43.83735,43.88855,45.04484,45.111,43.69183,45.37833,43.6472,45.26212,44.66697,43.51302,43.69985,43.42405,43.50834,44.95199,43.6919,43.63744,43.43144,44.69951,43.50658,45.13892,43.68822,44.69283,45.10628,44.68769,43.4204,43.68891,43.6772,43.66724,44.94892,43.673,45.40933,44.96536,45.72368,43.66106,44.68769,44.62727,44.62965,43.61895,45.20126,45.15177,45.01517,45.1233,45.1333,44.59527,44.95621,44.71402,45.14022,45.14101,43.641,45.12103,44.9856,43.63273,43.68505,43.64198,43.61047,45.25096,43.55112,43.69663,44.95698,44.58521,43.69835,44.97415,43.6186,43.69422,43.70401,43.62252,43.65461,43.62553,44.73491,45.1492,44.3334,43.42677,44.7083,44.5023,44.50182,45.20878,43.63436,45.71507,45.2669,45.11048,45.09923,45.1,45.0832,44.99921,43.48639,43.66999,43.67264,45.16516,44.69605,45.26793,45.12006,43.4647,44.61949,45,44.27258,43.59923,43.71557,44.61159,45.3667,43.62905,43.68616,44.2575,43.73882,45.3796,45.37942,43.49335,43.74912,43.63405,43.6772,44.61894,43.68241,43.70326,43.52035,43.50868,43.78343,43.72467,43.83205,43.50578,44.2605,45.2708,45.10362,45.10574,43.42055,44.97344,43.41084,44.58236,43.51516,44.61175,44.98887,43.63253,43.6283,45.33006,44.95833,44.97313,44.99147,43.47264,45.02376,43.50256,43.63685,43.633,45.38256,43.6296,44.97619,43.69172,44.95984,44.58356,45.41866,45.21372,44.97467,45.0073,43.67669,43.80858,43.52703,43.53301,44.61022,43.67633,44.60393,44.43992,43.51764,44.6325,44.60235,43.66345,44.99206,44.9766,44.93675,44.6167,44.70273,44.48513)
long=c(-65.82654,-66.76915,-64.25404,-65.9014,-65.90719,-65.7084,-65.6738,-65.67257,-65.6778,-64.9,-64.48189,-65.83812,-66.96382,-64.76276,-64.41178,-66.78266,-65.75105,-65.86791,-64.26228,-67.08128,-63.94631,-66.36808,-65.99769,-65.82789,-65.61631,-65.62322,-64.49627,-66.96304,-66.93141,-66.71888,-65.78074,-66.09383,-66.9969,-66.12741,-66.09718,-66.86069,-66.35931,-65.90693,-64.12124,-66.05395,-66.08877,-66.75014,-65.76929,-65.94188,-65.64708,-66.00485,-66.73269,-65.82077,-66.14861,-65.6245,-65.6109,-65.77518,-66.26114,-65.93082,-66.74722,-64.34153,-66.69499,-65.67671,-66.14406,-65.9948,-66.00251,-66.94392,-65.99518,-64.92706,-66.72582,-64.61453,-65.91562,-66.72309,-66.68641,-66.68477,-66.03735,-64.62047,-64.81232,-66.93072,-66.9964,-66.99933,-66.76369,-66.96656,-66.71938,-66.96113,-66.96551,-66.06152,-67.01127,-66.91766,-65.78451,-65.77797,-65.79008,-66.02289,-65.00188,-65.79455,-65.88197,-65.23964,-66.75834,-65.86214,-66.95249,-66.02373,-65.94689,-65.85686,-66.02926,-65.99359,-65.81501,-66.72604,-66.9577,-66.26667,-65.62647,-66.71053,-67.1013,-67.10187,-66.10616,-66.04112,-64.65026,-66.09046,-67.03546,-66.39665,-64.949,-64.9667,-66.90648,-65.98843,-66.05015,-66.05649,-66.23939,-66.71873,-66.07333,-66.54549,-65.98472,-66.76206,-66.99933,-66.31754,-66.02321,-65.89888,-66.81908,-64.332,-66.02703,-65.83184,-66.33866,-65.94848,-64.12557,-64.12941,-65.68482,-65.86594,-65.79096,-65.86615,-66.72928,-65.83945,-66.04713,-65.77216,-65.76416,-66.14067,-66.08676,-65.92331,-65.98543,-66.32979,-66.06732,-66.50543,-66.50797,-65.63906,-66.9132,-66.01256,-66.76968,-65.76324,-66.75236,-66.91457,-66.06356,-66.0573,-64.69175,-66.73,-66.90683,-66.94061,-65.71102,-66.93858,-65.77045,-65.82332,-65.82441,-64.21233,-65.82546,-66.90538,-65.8667,-66.7197,-66.76596,-64.92214,-66.10414,-66.92311,-65.13797,-66.01695,-66.00262,-65.76791,-65.77155,-66.84181,-65.97445,-66.84205,-66.01569,-65.78002,-66.69222,-66.80682,-65.86613,-66.87169,-66.70255,-66.73583,-66.83263,-66.7374,-66.85033)
data=data.frame(site,lat,long)
library(leaflet)
# start basemap (note the argument to hide the zoom buttons)
leaflet(options = leafletOptions(zoomControl = FALSE)) %>%
# add ocean basemap
addProviderTiles(providers$Esri.OceanBasemap) %>%
# focus map in a certain area / zoom level
setView(lng = -66.0418475, lat = 45.110292, zoom = 7) %>%
# add inset map
addMiniMap(
tiles = providers$Esri.OceanBasemap,
position = 'bottomright',
width = 100, height = 100,
toggleDisplay = FALSE) %>%
### Add scale bar
addScaleBar()%>%
# add points (as circle markers)
addCircleMarkers(data = data, ~long, ~lat,
weight = 0.5,
col = 'white',
fillColor = 'blue',
radius = 10,
fillOpacity = 0.9,
stroke = T)
When I knit this to html I get a map that looks like this, which is what I want it to look like in the PDF:
But when I knit this to a PDF it looks like this, you can notice the circle markers are cut off near the bottom center.
I've tried messing around with the zoom level and the setView, neither of which have worked. I've also tried messing around with the fig.height/fig.width/out.height/out.width settings, none of which worked (and also created blank grey areas in the map which is a whole other can of worms I'm trying to figure out).
I realize I should probably use a map package that isn't interactive like leaflet but at this point I've come too far so I would like to figure out why this is happening. Any help or advice would be greatly appreciated!
UPDATE: sessionInfo() output
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18363)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
[5] LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sp_1.4-4
loaded via a namespace (and not attached):
[1] pillar_1.5.0 compiler_4.0.3 tools_4.0.3 digest_0.6.27
evaluate_0.14 lifecycle_1.0.0 tibble_3.0.4 gtable_0.3.0
[9] lattice_0.20-41 pkgconfig_2.0.3 rlang_0.4.10 DBI_1.1.1
yaml_2.2.1 xfun_0.19 dplyr_1.0.4 stringr_1.4.0
[17] knitr_1.31 generics_0.1.0 vctrs_0.3.5 grid_4.0.3
tidyselect_1.1.0 glue_1.4.2 R6_2.5.0 fansi_0.4.1
[25] rmarkdown_2.7 purrr_0.3.4 tidyr_1.1.2 ggplot2_3.3.3
magrittr_2.0.1 scales_1.1.1 ellipsis_0.3.1 htmltools_0.5.1.1
[33] ggthemes_4.2.4 assertthat_0.2.1 colorspace_2.0-0 utf8_1.1.4
stringi_1.5.3 munsell_0.5.0 crayon_1.4.1
