tweak to plot routines

kingaa · Feb 14, 2024 · a53f722 · a53f722
1 parent 269116c
commit a53f722
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Showing 41 changed files with 8 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: phylopomp
 Type: Package
 Title: Phylodynamic Inference for POMP Models
-Version: 0.10.2.0
-Date: 2024-02-12
+Version: 0.10.3.0
+Date: 2024-02-14
 Authors@R: c(person(given=c("Aaron","A."),family="King",role=c("aut","cre"),email="[email protected]",comment=c(ORCID="0000-0001-6159-3207")),
 	  person(given=c("Qianying"),family="Lin",role=c("aut"),comment=c(ORCID="0000-0001-8620-9910"))
 	  )

diff --git a/R/treeplot.R b/R/treeplot.R
@@ -83,7 +83,8 @@ treeplot <- function (
     separate(label,into=c("nodecol","deme","label")) |>
     mutate(
       deme=if_else(deme=="NA",NA_character_,deme),
-      label=if_else(label=="NA",NA_character_,label)
+      label=if_else(label=="NA",NA_character_,label),
+      y=y-3
     ) -> dat
 
   ndeme <- max(1L,length(unique(dat$deme))-1L)
@@ -131,6 +132,7 @@ treeplot <- function (
     scale_alpha_manual(values=c(`TRUE`=1,`FALSE`=0))+
     guides(alpha="none",color="none")+
     expand_limits(x=c(dat$x,t0,time))+
+    coord_cartesian(ylim=c(0,NA),expand=TRUE,default=FALSE)+
     theme_tree2()+
     theme(...) -> pl
 

diff --git a/inst/NEWS b/inst/NEWS
@@ -14,6 +14,8 @@ _C_h_a_n_g_e_s _i_n '_p_h_y_l_o_p_o_m_p' _v_e_r_s_i_o_n
 
         • Parameter name changes in some of the examples.
 
+        • In plotting, trees are shifted down on the y axis.
+
 _C_h_a_n_g_e_s _i_n '_p_h_y_l_o_p_o_m_p' _v_e_r_s_i_o_n _0._9:
 
         • Inclusion of ‘pomp’ methods for SEIRS model.

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -7,6 +7,7 @@
     \item The genealogy description (\code{getInfo(description=TRUE)}) now reports both deme and lineage.
     \item \code{curtail()} more carefully rewinds the history.
     \item Parameter name changes in some of the examples.
+    \item In plotting, trees are shifted down on the y axis.
   }
 }
 \section{Changes in \pkg{phylopomp} version 0.9}{

diff --git a/tests/curtail-01.png b/tests/curtail-01.png
diff --git a/tests/diagram-07.png b/tests/diagram-07.png
diff --git a/tests/lbdp1-02.png b/tests/lbdp1-02.png
diff --git a/tests/lbdp1-03.png b/tests/lbdp1-03.png
diff --git a/tests/lbdp1-04.png b/tests/lbdp1-04.png
diff --git a/tests/lbdp2-01.png b/tests/lbdp2-01.png
diff --git a/tests/lbdp2-03.png b/tests/lbdp2-03.png
diff --git a/tests/lbdp2-04.png b/tests/lbdp2-04.png
diff --git a/tests/lbdp3-01.png b/tests/lbdp3-01.png
diff --git a/tests/lbdp3-02.png b/tests/lbdp3-02.png
diff --git a/tests/lbdp3-03.png b/tests/lbdp3-03.png
diff --git a/tests/lineages-02.png b/tests/lineages-02.png
diff --git a/tests/lineages-03.png b/tests/lineages-03.png
diff --git a/tests/moran1-01.png b/tests/moran1-01.png
diff --git a/tests/moran1-02.png b/tests/moran1-02.png
diff --git a/tests/parse-01.png b/tests/parse-01.png
diff --git a/tests/parse-02.png b/tests/parse-02.png
diff --git a/tests/parse-03.png b/tests/parse-03.png
diff --git a/tests/parse-04.png b/tests/parse-04.png
diff --git a/tests/parse-05.png b/tests/parse-05.png
diff --git a/tests/parse-06.png b/tests/parse-06.png
diff --git a/tests/parse-07.png b/tests/parse-07.png
diff --git a/tests/plot-01.png b/tests/plot-01.png
diff --git a/tests/seir1-01.png b/tests/seir1-01.png
diff --git a/tests/seir1-02.png b/tests/seir1-02.png
diff --git a/tests/seir2-01.png b/tests/seir2-01.png
diff --git a/tests/seir2-02.png b/tests/seir2-02.png
diff --git a/tests/seir2-03.png b/tests/seir2-03.png
diff --git a/tests/seir2-05.png b/tests/seir2-05.png
diff --git a/tests/si2r1-01.png b/tests/si2r1-01.png
diff --git a/tests/si2r1-02.png b/tests/si2r1-02.png
diff --git a/tests/si2r1-04.png b/tests/si2r1-04.png
diff --git a/tests/siir1-01.png b/tests/siir1-01.png
diff --git a/tests/siir1-02.png b/tests/siir1-02.png
diff --git a/tests/siir1-03.png b/tests/siir1-03.png
diff --git a/tests/sir1-01.png b/tests/sir1-01.png
diff --git a/tests/sir1-02.png b/tests/sir1-02.png