@@ -116,6 +116,8 @@ nodebar <- function(data, cols, color, alpha=1, position="stack") {

 ##' @param cols columns of the data.frame that store the stats

 ##' @param color set color of bars

 ##' @param alpha set transparency of the charts

+##' @param outline.color color of outline

+##' @param outline.size size of outline

 ##' @return list of ggplot objects

 ##' @export

 ##' @author Guangchuang Yu

@@ -119,7 +119,7 @@ nodebar <- function(data, cols, color, alpha=1, position="stack") {

 ##' @return list of ggplot objects

 ##' @export

 ##' @author Guangchuang Yu

-nodepie <- function(data, cols, color, alpha=1) {

+nodepie <- function(data, cols, color, alpha=1, outline.color="transparent", outline.size=0) {

     if (! "node" %in% colnames(data)) {

         stop("data should have a column 'node'...")

     }

@@ -128,14 +128,14 @@ nodepie <- function(data, cols, color, alpha=1) {

         color <- NA

     }

     ldf <- gather(data, type, value, !! cols) %>% split(., .$node)

-    lapply(ldf, function(df) ggpie(df, y=~value, fill=~type, color, alpha))

+    lapply(ldf, function(df) ggpie(df, y=~value, fill=~type, color, alpha, outline.color, outline.size))

 }

 ##' @importFrom methods missingArg

-ggpie <- function(data, y, fill, color, alpha=1) {

+ggpie <- function(data, y, fill, color, alpha=1, outline.color="transparent", outline.size=0) {

     p <- ggplot(data, aes_(x=1, y=y, fill=fill)) +

-        geom_bar(stat='identity', alpha=alpha) +

+        geom_bar(stat='identity', alpha=alpha, color=outline.color, size=outline.size, show.legend = F) +

         coord_polar(theta='y') + theme_inset()

     if (missingArg(color) || is.null(color) || is.na(color)) {

@@ -22,8 +22,6 @@

 ##' For demonstration of this function, please refer to chapter 8.3 of 

 ##' *Data Integration, Manipulation and Visualization of Phylogenetic Trees*

 ##' <http://yulab-smu.top/treedata-book/index.html> by Guangchuang Yu.

-##' 

-

 geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

                        x = "node", reverse_x = FALSE, reverse_y = FALSE) {

     structure(list(insets = insets, width = width, height = height,

@@ -37,7 +35,6 @@ geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

 ##' @title inset

 ##' @rdname inset

 ##' @param tree_view tree view 

-##' @inheritParams geom_inset

 ##' @return tree view with insets

 ##' @importFrom yulab.utils get_fun_from_pkg

 ##' @export

@@ -1,19 +1,29 @@

-##' add subplots to tree

-##'

+##' gemo_inset can add subplots to tree by accepting a list of ggplot objects that are ancestral 

+##' stats or data associated with selected nodes in the tree. These ggplot objects can be any 

+##' kind of charts or hybrid of of these charts.

+##' 

+##' Users can also use 

+##' 

 ##' 

 ##' @title geom_inset

 ##' @rdname inset

 ##' @param insets a list of ggplot objects, named by node number

-##' @param width width of inset, relative to the range of x-axis

-##' @param height height of inset, relative to the range of y-axis

-##' @param hjust horizontal adjustment

-##' @param vjust vertical adjustment

-##' @param x x position, one of 'node' and 'branch'

-##' @param reverse_x whether x axis was reversed by scale_x_reverse

-##' @param reverse_y whether y axis was reversed by scale_y_reverse

+##' @param width width of the inset, relative to the range of x-axis, defaults to .1

+##' @param height height of the inset, relative to the range of y-axis, defaults to .1

+##' @param hjust adjust the horizontal position of the charts, charts will go left if hjust > 0

+##' @param vjust adjust the vertical position of the charts, charts will go down if vjust > 0

+##' @param x the position where users want to place the charts, one of 'node' (default) and 'branch'

+##' @param reverse_x whether to reverse x axis of the charts by 'ggplot2::scale_x_reverse', defaults to 'FALSE'

+##' @param reverse_y whether to reverse y axis of the charts by 'ggplot2::scale_y_reverse', defaults to 'FALSE'

 ##' @return inset layer

 ##' @export

 ##' @author Guangchuang Yu

+##' @references

+##' For demonstration of this function, please refer to chapter 8.3 of 

+##' *Data Integration, Manipulation and Visualization of Phylogenetic Trees*

+##' <http://yulab-smu.top/treedata-book/index.html> by Guangchuang Yu.

+##' 

+

 geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

                        x = "node", reverse_x = FALSE, reverse_y = FALSE) {

     structure(list(insets = insets, width = width, height = height,

@@ -21,13 +31,13 @@ geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

                    reverse_x = reverse_x, reverse_y = reverse_y), class = "tree_inset")

 }

-##' add insets in a tree

+##' add subplots as insets in a tree

 ##'

 ##'

 ##' @title inset

 ##' @rdname inset

-##' @param tree_view tree view

-## @inheritParams geom_inset

+##' @param tree_view tree view 

+##' @inheritParams geom_inset

 ##' @return tree view with insets

 ##' @importFrom yulab.utils get_fun_from_pkg

 ##' @export

@@ -74,7 +84,7 @@ inset <- function(tree_view, insets, width, height, hjust=0, vjust=0,

 ##'

 ##'

 ##' @title nodebar

-##' @param position position of bar, one of 'stack' and 'dodge'

+##' @param position position of bars, if 'stack' (default) make bars stacked atop one another, 'dodge' make them dodged side-to-side

 ##' @inheritParams nodepie

 ##' @return list of ggplot objects

 ##' @export

@@ -105,10 +115,10 @@ nodebar <- function(data, cols, color, alpha=1, position="stack") {

 ##'

 ##'

 ##' @title nodepie

-##' @param data a data.frame of stats with an additional column of node number

-##' @param cols column of stats

-##' @param color color of bar

-##' @param alpha alpha

+##' @param data a data.frame of stats with an additional column of node number named "node"

+##' @param cols columns of the data.frame that store the stats

+##' @param color set color of bars

+##' @param alpha set transparency of the charts

 ##' @return list of ggplot objects

 ##' @export

 ##' @author Guangchuang Yu

@@ -29,7 +29,7 @@ geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

 ##' @param tree_view tree view

 ## @inheritParams geom_inset

 ##' @return tree view with insets

-##' @importFrom rvcheck get_fun_from_pkg

+##' @importFrom yulab.utils get_fun_from_pkg

 ##' @export

 ##' @author Guangchuang Yu

 inset <- function(tree_view, insets, width, height, hjust=0, vjust=0,

@@ -58,8 +58,8 @@ inset <- function(tree_view, insets, width, height, hjust=0, vjust=0,

     if (reverse_y)

         yy <- -yy

-    width <- width * diff(range(tree_view$data$x))

-    height <- height * diff(range(tree_view$data$y))

+    width <- width * diff(range(tree_view$data$x, na.rm = TRUE))

+    height <- height * diff(range(tree_view$data$y, na.rm = TRUE))

     geom_subview <- get_fun_from_pkg("ggimage", "geom_subview")

@@ -139,7 +139,3 @@ ggpie <- function(data, y, fill, color, alpha=1) {

     return(p)

 }

-

-

-

-

@@ -58,8 +58,8 @@ inset <- function(tree_view, insets, width, height, hjust=0, vjust=0,

     if (reverse_y)

         yy <- -yy

-    width <- width * diff(range(xx))

-    height <- height * diff(range(yy))

+    width <- width * diff(range(tree_view$data$x))

+    height <- height * diff(range(tree_view$data$y))

     geom_subview <- get_fun_from_pkg("ggimage", "geom_subview")

@@ -27,7 +27,7 @@ geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

 ##' @title inset

 ##' @rdname inset

 ##' @param tree_view tree view

-##' @inheritParams geom_inset

+## @inheritParams geom_inset

 ##' @return tree view with insets

 ##' @importFrom rvcheck get_fun_from_pkg

 ##' @export

@@ -1,16 +1,33 @@

-##' add insets in a tree

-##'

+##' add subplots to tree

 ##'

-##' @title inset

-##' @param tree_view tree view

+##' 

+##' @title geom_inset

+##' @rdname inset

 ##' @param insets a list of ggplot objects, named by node number

-##' @param width width of inset

-##' @param height height of inset

+##' @param width width of inset, relative to the range of x-axis

+##' @param height height of inset, relative to the range of y-axis

 ##' @param hjust horizontal adjustment

 ##' @param vjust vertical adjustment

 ##' @param x x position, one of 'node' and 'branch'

 ##' @param reverse_x whether x axis was reversed by scale_x_reverse

 ##' @param reverse_y whether y axis was reversed by scale_y_reverse

+##' @return inset layer

+##' @export

+##' @author Guangchuang Yu

+geom_inset <- function(insets, width = .1, height = .1, hjust = 0, vjust = 0,

+                       x = "node", reverse_x = FALSE, reverse_y = FALSE) {

+    structure(list(insets = insets, width = width, height = height,

+                   hjust = hjust, vjust = vjust, x = x,

+                   reverse_x = reverse_x, reverse_y = reverse_y), class = "tree_inset")

+}

+

+##' add insets in a tree

+##'

+##'

+##' @title inset

+##' @rdname inset

+##' @param tree_view tree view

+##' @inheritParams geom_inset

 ##' @return tree view with insets

 ##' @importFrom rvcheck get_fun_from_pkg

 ##' @export

@@ -18,6 +35,12 @@

 inset <- function(tree_view, insets, width, height, hjust=0, vjust=0,

                   x="node", reverse_x=FALSE, reverse_y=FALSE) {

+    if(width < 0 || width > 1)

+        stop("width should be in range of (0,1)")

+

+    if(height < 0 || height > 1)

+        stop("height should be in range of (0,1)")

+

     df <- tree_view$data[as.numeric(names(insets)),]

     x <- match.arg(x, c("node", "branch", "edge"))

@@ -35,6 +58,9 @@ inset <- function(tree_view, insets, width, height, hjust=0, vjust=0,

     if (reverse_y)

         yy <- -yy

+    width <- width * diff(range(xx))

+    height <- height * diff(range(yy))

+

     geom_subview <- get_fun_from_pkg("ggimage", "geom_subview")

     tree_view + geom_subview(subview = insets,

@@ -12,6 +12,7 @@

 ##' @param reverse_x whether x axis was reversed by scale_x_reverse

 ##' @param reverse_y whether y axis was reversed by scale_y_reverse

 ##' @return tree view with insets

+##' @importFrom rvcheck get_fun_from_pkg

 ##' @export

 ##' @author Guangchuang Yu

 inset <- function(tree_view, insets, width, height, hjust=0, vjust=0,

@@ -14,7 +14,7 @@

 ##' @return tree view with insets

 ##' @export

 ##' @author Guangchuang Yu

-inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,

+inset <- function(tree_view, insets, width, height, hjust=0, vjust=0,

                   x="node", reverse_x=FALSE, reverse_y=FALSE) {

     df <- tree_view$data[as.numeric(names(insets)),]

@@ -17,8 +17,6 @@

 inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,

                   x="node", reverse_x=FALSE, reverse_y=FALSE) {

-    message("The inset function will be defunct in next release, please use ggimage::geom_subview() instead.")

-

     df <- tree_view$data[as.numeric(names(insets)),]

     x <- match.arg(x, c("node", "branch", "edge"))

@@ -36,14 +36,13 @@ inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,

     if (reverse_y)

         yy <- -yy

-    for (i in seq_along(insets)) {

-        tree_view %<>% subview(insets[[i]],

-                               x = xx[i],

-                               y = yy[i],

-                               width = width,

-                               height = height)

-    }

-    return(tree_view)

+    geom_subview <- get_fun_from_pkg("ggimage", "geom_subview")

+

+    tree_view + geom_subview(subview = insets,

+                            width = width,

+                            height = height,

+                            x = xx,

+                            y = yy)

 }

 ##' generate a list of bar charts for results of ancestral state reconstruction

@@ -63,7 +63,7 @@ nodebar <- function(data, cols, color, alpha=1, position="stack") {

     }

     type <- value <- NULL

-    ldf <- gather(data, type, value, cols) %>% split(., .$node)

+    ldf <- gather(data, type, value, !! cols) %>% split(., .$node)

     bars <- lapply(ldf, function(df) ggplot(df, aes_(x=1, y=~value, fill=~type)) +

                                      geom_bar(stat='identity', alpha=alpha, position=position) +

                                      theme_inset()

@@ -96,7 +96,7 @@ nodepie <- function(data, cols, color, alpha=1) {

     if (missingArg(color)) {

         color <- NA

     }

-    ldf <- gather(data, type, value, cols) %>% split(., .$node)

+    ldf <- gather(data, type, value, !! cols) %>% split(., .$node)

     lapply(ldf, function(df) ggpie(df, y=~value, fill=~type, color, alpha))

 }

@@ -17,6 +17,8 @@

 inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,

                   x="node", reverse_x=FALSE, reverse_y=FALSE) {

+    message("The inset function will be defunct in next release, please use ggimage::geom_subview() instead.")

+

     df <- tree_view$data[as.numeric(names(insets)),]

     x <- match.arg(x, c("node", "branch", "edge"))

@@ -9,10 +9,14 @@

 ##' @param hjust horizontal adjustment

 ##' @param vjust vertical adjustment

 ##' @param x x position, one of 'node' and 'branch'

+##' @param reverse_x whether x axis was reversed by scale_x_reverse

+##' @param reverse_y whether y axis was reversed by scale_y_reverse

 ##' @return tree view with insets

 ##' @export

 ##' @author Guangchuang Yu

-inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x="node") {

+inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0,

+                  x="node", reverse_x=FALSE, reverse_y=FALSE) {

+

     df <- tree_view$data[as.numeric(names(insets)),]

     x <- match.arg(x, c("node", "branch", "edge"))

@@ -25,6 +29,10 @@ inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x=

     xx <- xx - hjust

     yy <- yy - vjust

+    if (reverse_x)

+        xx <- -xx

+    if (reverse_y)

+        yy <- -yy

     for (i in seq_along(insets)) {

         tree_view %<>% subview(insets[[i]],

@@ -1,6 +1,6 @@

 ##' add insets in a tree

 ##'

-##' 

+##'

 ##' @title inset

 ##' @param tree_view tree view

 ##' @param insets a list of ggplot objects, named by node number

@@ -22,7 +22,7 @@ inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x=

         xx <- df$branch

     }

     yy <- df$y

-    

+

     xx <- xx - hjust

     yy <- yy - vjust

@@ -38,7 +38,7 @@ inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x=

 ##' generate a list of bar charts for results of ancestral state reconstruction

 ##'

-##' 

+##'

 ##' @title nodebar

 ##' @param position position of bar, one of 'stack' and 'dodge'

 ##' @inheritParams nodepie

@@ -52,7 +52,7 @@ nodebar <- function(data, cols, color, alpha=1, position="stack") {

         stop("data should have a column 'node'...")

     }

     type <- value <- NULL

-    

+

     ldf <- gather(data, type, value, cols) %>% split(., .$node)

     bars <- lapply(ldf, function(df) ggplot(df, aes_(x=1, y=~value, fill=~type)) +

                                      geom_bar(stat='identity', alpha=alpha, position=position) +

@@ -69,7 +69,7 @@ nodebar <- function(data, cols, color, alpha=1, position="stack") {

 ##' generate a list of pie charts for results of ancestral stat reconstruction

 ##'

-##' 

+##'

 ##' @title nodepie

 ##' @param data a data.frame of stats with an additional column of node number

 ##' @param cols column of stats

@@ -91,11 +91,12 @@ nodepie <- function(data, cols, color, alpha=1) {

 }

+##' @importFrom methods missingArg

 ggpie <- function(data, y, fill, color, alpha=1) {

     p <- ggplot(data, aes_(x=1, y=y, fill=fill)) +

         geom_bar(stat='identity', alpha=alpha) +

         coord_polar(theta='y') + theme_inset()

-    

+

     if (missingArg(color) || is.null(color) || is.na(color)) {

         ## do nothing

     } else {

@@ -12,7 +12,7 @@

 ##' @return tree view with insets

 ##' @export

 ##' @author Guangchuang Yu

-inset <- function(tree_view, insets, width=0.05, height=0.05, hjust=0, vjust=0, x="node") {

+inset <- function(tree_view, insets, width=0.1, height=0.1, hjust=0, vjust=0, x="node") {

     df <- tree_view$data[as.numeric(names(insets)),]

     x <- match.arg(x, c("node", "branch", "edge"))

@@ -13,7 +13,7 @@

 ##' @export

 ##' @author Guangchuang Yu

 inset <- function(tree_view, insets, width=0.05, height=0.05, hjust=0, vjust=0, x="node") {

-    df <- tree_view$data[names(insets),]

+    df <- tree_view$data[as.numeric(names(insets)),]

     x <- match.arg(x, c("node", "branch", "edge"))

     if (x == 'node') {

new file mode 100644

@@ -0,0 +1,110 @@

+##' add insets in a tree

+##'

+##' 

+##' @title inset

+##' @param tree_view tree view

+##' @param insets a list of ggplot objects, named by node number

+##' @param width width of inset

+##' @param height height of inset

+##' @param hjust horizontal adjustment

+##' @param vjust vertical adjustment

+##' @param x x position, one of 'node' and 'branch'

+##' @return tree view with insets

+##' @export

+##' @author Guangchuang Yu

+inset <- function(tree_view, insets, width=0.05, height=0.05, hjust=0, vjust=0, x="node") {

+    df <- tree_view$data[names(insets),]

+    x <- match.arg(x, c("node", "branch", "edge"))

+

+    if (x == 'node') {

+        xx <- df$x

+    } else {

+        xx <- df$branch

+    }

+    yy <- df$y

+    

+    xx <- xx - hjust

+    yy <- yy - vjust

+

+    for (i in seq_along(insets)) {

+        tree_view %<>% subview(insets[[i]],

+                               x = xx[i],

+                               y = yy[i],

+                               width = width,

+                               height = height)

+    }

+    return(tree_view)

+}

+

+##' generate a list of bar charts for results of ancestral state reconstruction

+##'

+##' 

+##' @title nodebar

+##' @param position position of bar, one of 'stack' and 'dodge'

+##' @inheritParams nodepie

+##' @return list of ggplot objects

+##' @export

+##' @importFrom ggplot2 geom_bar

+##' @importFrom tidyr gather

+##' @author Guangchuang Yu

+nodebar <- function(data, cols, color, alpha=1, position="stack") {

+    if (! "node" %in% colnames(data)) {

+        stop("data should have a column 'node'...")

+    }

+    type <- value <- NULL

+    

+    ldf <- gather(data, type, value, cols) %>% split(., .$node)

+    bars <- lapply(ldf, function(df) ggplot(df, aes_(x=1, y=~value, fill=~type)) +

+                                     geom_bar(stat='identity', alpha=alpha, position=position) +

+                                     theme_inset()

+                   )

+

+    if (missingArg(color) || is.null(color) || is.na(color)) {

+        ## do nothing

+    } else {

+        bars <- lapply(bars, function(p) p+scale_fill_manual(values=color))

+    }

+    return(bars)

+}

+

+##' generate a list of pie charts for results of ancestral stat reconstruction

+##'

+##' 

+##' @title nodepie

+##' @param data a data.frame of stats with an additional column of node number

+##' @param cols column of stats

+##' @param color color of bar

+##' @param alpha alpha

+##' @return list of ggplot objects

+##' @export

+##' @author Guangchuang Yu

+nodepie <- function(data, cols, color, alpha=1) {

+    if (! "node" %in% colnames(data)) {

+        stop("data should have a column 'node'...")

+    }

+    type <- value <- NULL

+    if (missingArg(color)) {

+        color <- NA

+    }

+    ldf <- gather(data, type, value, cols) %>% split(., .$node)

+    lapply(ldf, function(df) ggpie(df, y=~value, fill=~type, color, alpha))

+}

+

+

+ggpie <- function(data, y, fill, color, alpha=1) {

+    p <- ggplot(data, aes_(x=1, y=y, fill=fill)) +

+        geom_bar(stat='identity', alpha=alpha) +

+        coord_polar(theta='y') + theme_inset()

+    

+    if (missingArg(color) || is.null(color) || is.na(color)) {

+        ## do nothing

+    } else {

+        p <- p+scale_fill_manual(values=color)

+    }

+    return(p)

+}

+

+

+

+

+