Browse code

facet_plot

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@120776 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 07/09/2016 01:36:05
Showing15 changed files

... ...
@@ -1,7 +1,7 @@
1 1
 Package: ggtree
2 2
 Type: Package
3 3
 Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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-Version: 1.5.12
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+Version: 1.5.13
5 5
 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
7 7
 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
... ...
@@ -22,6 +22,7 @@ S3method(fortify,r8s)
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 S3method(fortify,raxml)
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 S3method(identify,gg)
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 S3method(print,beastList)
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+export("%+>%")
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 export("%<%")
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 export("%<+%")
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 export("%>%")
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@@ -38,6 +39,7 @@ export(collapse)
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 export(decimal2Date)
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 export(download.phylopic)
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 export(expand)
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+export(facet_plot)
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 export(flip)
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 export(geom_aline)
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 export(geom_balance)
... ...
@@ -182,6 +184,7 @@ importFrom(ggplot2,draw_key_text)
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 importFrom(ggplot2,element_blank)
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 importFrom(ggplot2,element_line)
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 importFrom(ggplot2,element_rect)
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+importFrom(ggplot2,facet_grid)
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 importFrom(ggplot2,fortify)
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 importFrom(ggplot2,geom_bar)
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 importFrom(ggplot2,geom_rect)
... ...
@@ -1,5 +1,16 @@
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+CHANGES IN VERSION 1.5.13
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+------------------------
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+ o facet_plot for plotting data with tree <2016-09-06, Tue>
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+ o more parameters for column names in gheatmap <2016-09-06, Tue>
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+   + colnames_angle
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+   + colnames_offset_x
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+   + colnames_offset_y
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+   + hjust
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+ o offset parameter in geom_tiplab and geom_tiplab2 <2016-09-05, Mon>
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+ 
1 11
 CHANGES IN VERSION 1.5.12
2 12
 ------------------------
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+ o use data in all layers instead of the base layer for coordination calculation in subview <2016-09-01, Thu>
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  o bug fixed in subview, width & height should be width/2 & height/2 <2016-09-01, Thu>
4 15
  
5 16
 CHANGES IN VERSION 1.5.11
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new file mode 100644
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@@ -0,0 +1,29 @@
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+##' plot tree associated data in an additional panel
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+##'
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+##' 
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+##' @title facet_plot
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+##' @param p tree view
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+##' @param panel panel name for plot of input data
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+##' @param data data to plot by 'geom', first column should be matched with tip label of tree
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+##' @param geom geom function to plot the data
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+##' @param mapping aes mapping for 'geom'
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+##' @param ... additional parameters for 'geom'
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+##' @return ggplot object
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+##' @export
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+##' @author Guangchuang Yu
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+facet_plot <- function(p, panel, data, geom, mapping=NULL, ...) {
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+    p <- add_panel(p, panel)
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+    df <- p %+>% data
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+    p + geom(data=df, mapping=mapping, ...)
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+}
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+
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+##' @importFrom ggplot2 facet_grid
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+add_panel <- function(p, panel) {
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+    df <- p$data
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+    if (is.null(df$panel)) {
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+        df$panel <- factor("Tree")
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+    }
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+    levels(df$panel) %<>% c(., panel)
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+    p$data <- df
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+    p + facet_grid(.~panel, scales="free_x")
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+}
... ...
@@ -4,6 +4,7 @@
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 ##' @title geom_tiplab 
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 ##' @param mapping aes mapping
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 ##' @param hjust horizontal adjustment
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+##' @param offset tiplab offset
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 ##' @param align align tip lab or not, logical
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 ##' @param linetype linetype for adding line if align = TRUE
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 ##' @param linesize line size of line if align = TRUE
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@@ -17,9 +18,13 @@
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 ##' require(ape)
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 ##' tr <- rtree(10)
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 ##' ggtree(tr) + geom_tiplab()
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-geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dotted", linesize=1, geom="text", ...) {
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+geom_tiplab <- function(mapping=NULL, hjust = 0,  align = FALSE, linetype = "dotted", linesize=1, geom="text", offset = 0, ...) {
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     geom <- match.arg(geom, c("text", "label"))
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-
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+    if (geom == "text") {
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+        text_geom <- geom_text2
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+    } else {
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+        text_geom <- geom_label2
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+    }
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     x <- y <- label <- isTip <- NULL
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     if (align == TRUE) {
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         self_mapping <- aes(x = max(x, na.rm=TRUE) + diff(range(x, na.rm=TRUE))/200, y = y, label = label, subset= isTip)
... ...
@@ -34,26 +39,21 @@ geom_tiplab <- function(mapping=NULL, hjust = 0, align = FALSE, linetype = "dott
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         text_mapping <- modifyList(self_mapping, mapping)
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     }
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-    dot_mapping <- NULL
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-    if (align && (!is.na(linetype) && !is.null(linetype))) {
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-        dot_mapping <- aes(xend=x+diff(range(x, na.rm=TRUE))/200, x=max(x, na.rm=TRUE), y=y, yend=y, subset=isTip)
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-        if (!is.null(mapping)) {
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-            dot_mapping <- modifyList(dot_mapping, mapping)
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-        }
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-    } 
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+    show_segment <- FALSE
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+    if (align && (!is.na(linetype) && !is.null(linetype))) {
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+        show_segment <- TRUE
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+    }  
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+
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     list(
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-        if (geom == "text") {
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-            geom_text2(mapping=text_mapping, 
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-                       hjust = hjust, ...)
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-        } else {
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-            geom_label2(mapping=text_mapping, 
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-                        hjust = hjust, ...)
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-        },
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-        if (!is.null(dot_mapping))
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-            geom_segment2(mapping=dot_mapping,
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-                          linetype = linetype,
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-                          size = linesize, ...)
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+        text_geom(mapping=text_mapping, 
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+                  hjust = hjust, nudge_x = offset, ...)
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+        ,
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+        if (show_segment)
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+            geom_tipsegment(mapping = aes(subset=isTip),
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+                            offset = offset,
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+                            linetype = linetype,
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+                            size = linesize, ...)
57 57
     )
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 }
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... ...
@@ -86,3 +86,46 @@ geom_tiplab2 <- function(mapping=NULL, hjust=0, ...) {
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          geom_tiplab(m2, hjust=1-hjust, ...)
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          )
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 }
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+
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+geom_tipsegment <- function(mapping=NULL, data=NULL,
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+                            geom=GeomSegmentGGtree, position = "identity",
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+                            offset,  ...,
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+                            show.legend=NA, inherit.aes=FALSE, na.rm=TRUE) {
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+    
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+    default_aes <- aes_(x=~x, y=~y)
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+    if (is.null(mapping)) {
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+        mapping <- default_aes
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+    } else {
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+        mapping <- modifyList(default_aes, mapping)
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+    }
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+    
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+    layer(stat=StatTipSegment,
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+          data = data,
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+          mapping = mapping,
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+          geom = geom,
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+          position = position,
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+          show.legend = show.legend,
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+          inherit.aes = inherit.aes,
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+          params = list(offset = offset,
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+                        na.rm = na.rm,
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+                        ...)
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+          )
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+}
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+
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+StatTipSegment <- ggproto("StatTipSegment", Stat,
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+                        compute_group = function(self, data, scales, params, offset) {
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+                            get_tipsegment_position(data, offset)
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+                        },
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+                        required_aes = c("x", "y")
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+                        )
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+
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+
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+get_tipsegment_position <- function(data, offset, adjustRatio=1/200) {
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+    adjust <- diff(range(data$x, na.rm=TRUE)) * adjustRatio
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+    xend <- data$x + adjust
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+    x <- max(data$x, na.rm = TRUE)  + offset
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+    y <- data$y
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+    data.frame(x=x, xend=xend, y=y, yend=y)
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+}
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+
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+
... ...
@@ -11,8 +11,12 @@
11 11
 ##' @param color color of heatmap cell border
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 ##' @param colnames logical, add matrix colnames or not
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 ##' @param colnames_position one of 'bottom' or 'top'
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+##' @param colnames_angle angle of column names
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 ##' @param colnames_level levels of colnames
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+##' @param colnames_offset_x x offset for column names
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+##' @param colnames_offset_y y offset for column names
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 ##' @param font.size font size of matrix colnames
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+##' @param hjust hjust for column names (0: align left, 0.5: align center, 1: align righ)
16 20
 ##' @return tree view
17 21
 ##' @importFrom ggplot2 geom_tile
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 ##' @importFrom ggplot2 geom_text
... ...
@@ -25,7 +29,8 @@
25 29
 ##' @export
26 30
 ##' @author Guangchuang Yu
27 31
 gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color="white",
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-                     colnames=TRUE, colnames_position="bottom", colnames_level=NULL, font.size=4) {
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+                     colnames=TRUE, colnames_position="bottom", colnames_angle=0, colnames_level=NULL,
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+                     colnames_offset_x = 0, colnames_offset_y = 0, font.size=4, hjust=0.5) {
29 34
     
30 35
     colnames_position %<>% match.arg(c("bottom", "top"))
31 36
     variable <- value <- lab <- y <- NULL
... ...
@@ -85,7 +90,9 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
85 90
         } else {
86 91
             y <- max(p$data$y) + 1
87 92
         }
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-        p2 <- p2 + geom_text(data=mapping, aes(x=to, label=from), y=y, size=font.size, inherit.aes = FALSE)
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+        mapping$y <- y
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+        p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=from), size=font.size, inherit.aes = FALSE,
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+                             angle=colnames_angle, nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)
89 96
     }
90 97
     
91 98
     p2 <- p2 + theme(legend.position="right", legend.title=element_blank())
... ...
@@ -88,6 +88,25 @@
88 88
     return(dd)
89 89
 }
90 90
 
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+##' update data with tree info (y coordination and panel)
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+##'
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+##'
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+##' @rdname add_TREEINFO
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+##' @title \%+>\%
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+##' @param p tree view 
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+##' @param data data.frame
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+##' @return updated data.frame
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+##' @export
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+##' @author Guangchuang Yu
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+`%+>%` <- function(p, data) {
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+    df <- p$data
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+    res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1, all.x=TRUE)
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+    lv <- levels(df$panel)
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+    res$panel <- factor(lv[length(lv)], levels=lv)
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+    return(res)
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+}
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+
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+
91 110
 ##' pipe
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 ##' @importFrom magrittr %>%
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 ##' @name %>%
... ...
@@ -18,8 +18,46 @@ subview <- function(mainview, subview, x, y, width=.1, height=.1) {
18 18
     aes_x <- mapping["x"]
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     aes_y <- mapping["y"]
20 20
     
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-    xrng <- mainview$data[, aes_x] %>% range %>% diff
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-    yrng <- mainview$data[, aes_y] %>% range %>% diff
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+    xrng <- mainview$data[, aes_x] %>% range 
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+    yrng <- mainview$data[, aes_y] %>% range
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+
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+    for (i in seq_along(mainview$layers)) {
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+        layer <- mainview$layers[[i]]
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+        dd <- layer$data
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+        if (is(dd, "data.frame")) {
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+            mapping <- as.character(layer$mapping)
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+            mn <- names(mapping)
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+            if ('x' %in% mn) {
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+                aes_x <- mapping["x"]
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+                xrng <- c(xrng, layer$data[, aes_x])
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+            }
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+            if ('xmin' %in% mn) {
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+                aes_x <- mapping["xmin"]
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+                xrng <- c(xrng, layer$data[, aes_x])
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+            }
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+            if ('xmax' %in% mn) {
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+                aes_x <- mapping["xmax"]
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+                xrng <- c(xrng, layer$data[, aes_x])
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+            }
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+            if ('y' %in% mn) {
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+                aes_y <- mapping["y"]
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+                yrng <- c(yrng, layer$data[, aes_y])
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+            }
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+            if ('ymin' %in% mn) {
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+                aes_y <- mapping["ymin"]
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+                yrng <- c(yrng, layer$data[, aes_y])
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+            }
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+            if ('ymax' %in% mn) {
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+                aes_y <- mapping["ymax"]
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+                yrng <- c(yrng, layer$data[, aes_y])
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+            }
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+            xrng <- range(xrng)
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+            yrng <- range(yrng)
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+        }
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+    }
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+
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+    xrng <- diff(xrng)
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+    yrng <- diff(yrng)
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     if (!any(class(subview) %in% c("ggplot", "grob", "character"))) {
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         stop("subview should be a ggplot or grob object, or an image file...")
... ...
@@ -382,6 +382,7 @@ is.tree <- function(x) {
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                         "baseml",
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                         "paml_rst",
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                         "baseml_mlc",
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+                        "codeml_mlc",
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                         "codeml",
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                         "hyphy",
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                         "beast")
... ...
@@ -1,11 +1,11 @@
1 1
 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
2 2
 ===========================================================================================================================
3 3
 
4
-[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
4
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.20-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.13-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-12850/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1122/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
5 5
 
6
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--09--01-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers)
6
+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--09--07-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
7 7
 
8
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.18-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.12-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)
8
+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
9 9
 
10 10
 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
11 11
 
... ...
@@ -17,7 +17,7 @@ Please cite the following article when using `ggtree`:
17 17
 
18 18
 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. *accepted*
19 19
 
20
-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-128-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
20
+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-140-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
21 21
 
22 22
 ------------------------------------------------------------------------
23 23
 
... ...
@@ -30,30 +30,30 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
30 30
 
31 31
 ### Download stats
32 32
 
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-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-12736/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1091/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-12850/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1122/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
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-         +---------------------------+---------------------------+----------------------------+--------+
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-         |                                                                                    *        |
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+         +--------------------------+--------------------------+--------------------------+------------+
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          |                                                                                             |
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-         |                                    *                                                        |
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-     400 +                           *   *                                                             +
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-         |                      *                                                                      |
50
+         |                                   *                                                         |
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+     400 +                         *    *                                                              +
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+         |                     *                                                                       |
53 53
          |                                                                                             |
54
-     200 +                 *                                                                           +
54
+     200 +                *                                                                            +
55 55
          |                                                                                             |
56 56
          |                                                                                             |
57
-         |   *    *   *                                                                                |
58
-       0 +---------------------------+---------------------------+----------------------------+--------+
59
-                                  2015.5                       2016                        2016.5
57
+         |   *   *    *                                                                                |
58
+       0 +--------------------------+--------------------------+--------------------------+------------+
59
+                                 2015.5                      2016                      2016.5
60 60
new file mode 100644
... ...
@@ -0,0 +1,23 @@
1
+% Generated by roxygen2: do not edit by hand
2
+% Please edit documentation in R/operator.R
3
+\name{\%+>\%}
4
+\alias{\%+>\%}
5
+\title{\%+>\%}
6
+\usage{
7
+p \%+>\% data
8
+}
9
+\arguments{
10
+\item{p}{tree view}
11
+
12
+\item{data}{data.frame}
13
+}
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+\value{
15
+updated data.frame
16
+}
17
+\description{
18
+update data with tree info (y coordination and panel)
19
+}
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+\author{
21
+Guangchuang Yu
22
+}
23
+
0 24
new file mode 100644
... ...
@@ -0,0 +1,31 @@
1
+% Generated by roxygen2: do not edit by hand
2
+% Please edit documentation in R/facet_plot.R
3
+\name{facet_plot}
4
+\alias{facet_plot}
5
+\title{facet_plot}
6
+\usage{
7
+facet_plot(p, panel, data, geom, mapping = NULL, ...)
8
+}
9
+\arguments{
10
+\item{p}{tree view}
11
+
12
+\item{panel}{panel name for plot of input data}
13
+
14
+\item{data}{data to plot by 'geom', first column should be matched with tip label of tree}
15
+
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+\item{geom}{geom function to plot the data}
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+
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+\item{mapping}{aes mapping for 'geom'}
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+
20
+\item{...}{additional parameters for 'geom'}
21
+}
22
+\value{
23
+ggplot object
24
+}
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+\description{
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+plot tree associated data in an additional panel
27
+}
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+\author{
29
+Guangchuang Yu
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+}
31
+
... ...
@@ -5,7 +5,7 @@
5 5
 \title{geom_tiplab}
6 6
 \usage{
7 7
 geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
8
-  linetype = "dotted", linesize = 1, geom = "text", ...)
8
+  linetype = "dotted", linesize = 1, geom = "text", offset = 0, ...)
9 9
 }
10 10
 \arguments{
11 11
 \item{mapping}{aes mapping}
... ...
@@ -20,6 +20,8 @@ geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,
20 20
 
21 21
 \item{geom}{one of 'text' and 'label'}
22 22
 
23
+\item{offset}{tiplab offset}
24
+
23 25
 \item{...}{additional parameter}
24 26
 }
25 27
 \value{
... ...
@@ -6,7 +6,8 @@
6 6
 \usage{
7 7
 gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
8 8
   color = "white", colnames = TRUE, colnames_position = "bottom",
9
-  colnames_level = NULL, font.size = 4)
9
+  colnames_angle = 0, colnames_level = NULL, colnames_offset_x = 0,
10
+  colnames_offset_y = 0, font.size = 4, hjust = 0.5)
10 11
 }
11 12
 \arguments{
12 13
 \item{p}{tree view}
... ...
@@ -27,9 +28,17 @@ gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",
27 28
 
28 29
 \item{colnames_position}{one of 'bottom' or 'top'}
29 30
 
31
+\item{colnames_angle}{angle of column names}
32
+
30 33
 \item{colnames_level}{levels of colnames}
31 34
 
35
+\item{colnames_offset_x}{x offset for column names}
36
+
37
+\item{colnames_offset_y}{y offset for column names}
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+
32 39
 \item{font.size}{font size of matrix colnames}
40
+
41
+\item{hjust}{hjust for column names (0: align left, 0.5: align center, 1: align righ)}
33 42
 }
34 43
 \value{
35 44
 tree view
... ...
@@ -182,24 +182,20 @@ inset(p, img)
182 182
 
183 183
 ![](figures/inset_img.png)
184 184
 
185
-# Align tree with other plots on a page
185
+# Plot tree with associated data
186 186
 
187
-This is currently difficult to achieve in `ggplot2`. However, it is possible to obtain good results by creating a dummy faceting of data.
187
+For associating phylogenetic tree with different type of plot produced by user's data, `ggtree` provides `facet_plot` function which accepts an input `data.frame` and a 'geom' function to draw the input data. The data will be displayed in an additional panel of the plot.
188 188
 
189 189
 ```{r warning=F, fig.width=10, fig.height=6}
190 190
 tr <- rtree(30)
191
-df <- fortify(tr)
192
-df$tipstats <- NA
193
-d1 <- df
194
-d2 <- df
195
-d2$tipstats[d2$isTip] <- abs(rnorm(30))
196
-d1$panel <- 'Tree'
197
-d2$panel <- 'Stats'
198
-d1$panel <- factor(d1$panel, levels=c("Tree", "Stats"))
199
-d2$panel <- factor(d2$panel, levels=c("Tree", "Stats"))
200
-
201
-p <- ggplot(mapping=aes(x=x, y=y)) + facet_grid(.~panel, scale="free_x") + theme_tree2()
202
-p+geom_tree(data=d1) + geom_point(data=d2, aes(x=tipstats)) 
191
+
192
+d1 <- data.frame(id=tr$tip.label, val=rnorm(30, sd=3))
193
+p <- ggtree(tr)
194
+
195
+p2 <- facet_plot(p, panel="dot", data=d1, geom=geom_point, aes(x=val), color='firebrick')
196
+d2 <- data.frame(id=tr$tip.label, value = abs(rnorm(30, mean=100, sd=50)))
197
+
198
+facet_plot(p2, panel='bar', data=d2, geom=geom_segment, aes(x=0, xend=value, y=y, yend=y), size=3, color='steelblue') + theme_tree2()
203 199
 ```
204 200
 
205 201
 # Tree annotation with Phylopic