diff --git a/README.Rmd b/README.Rmd
index 6d3d9f24..84ba0e84 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -13,15 +13,6 @@ knitr::opts_chunk$set(
)
```
-# ggheat
-
-
-[](https://github.com/Yunuuuu/ggheat/actions/workflows/R-CMD-check.yaml)
-
-
-This package is a `ggplot2` extension for heatmap. It utilizes the grammar of
-graphics to construct the heatmap and heatmap annotations.
-
## Installation
You can install the development version of ggheat from [GitHub](https://github.com/) with:
@@ -30,385 +21,3 @@ You can install the development version of ggheat from [GitHub](https://github.c
# install.packages("devtools")
pak::pkg_install("Yunuuuu/ggheat")
```
-
-
-```{r setup}
-library(ggheat)
-```
-
-Let's begin by creating some example data
-
-```{r setup_dat}
-set.seed(123)
-small_mat <- matrix(rnorm(81), nrow = 9)
-rownames(small_mat) <- paste0("row", seq_len(nrow(small_mat)))
-colnames(small_mat) <- paste0("column", seq_len(ncol(small_mat)))
-```
-
-## `ggheat`
-The core function in the `ggheat` package is `ggheat`, which sets the default data
-and mapping for the heatmap. Creating a simple heatmap is effortless with the
-`ggheat` function
-
-```{r}
-ggheat(small_mat)
-```
-
-The data can be a numeric or character vector, a data frame, and any other data
-which can be converted into a matrix. Simple vector will be converted into a one
-column matrix. They will all converted into the long formated data frame when
-drawing. The default mapping will use `aes(.data$.x, .data$.y)`, but can be
-controlled using `mapping` argument. The data in the underlying ggplot object
-contains following columns:
-
- - `.row_panel` or `.column_panl` instead of a column `.panel` since
- annotation can only have one facet axiss: the row panel
-
- - `.column_panel`: the column panel
-
- - `.row_names` and `.column_names`: the row and column names of the original
- matrix (only applicable when names exist).
-
- - `.row_index` and `.column_index`: the row and column index of the original
- matrix.
-
- - `.x` and `.y`: the `x` and `y` coordinates
-
- - `value`: the actual matrix value.
-
-```{r}
-ggheat(letters)
-```
-
-```{r}
-ggheat(1:10)
-```
-
-You can then add all other ggplot2 elements like `geoms`, `scales` and `facets`.
-
-```{r}
-ggheat(small_mat) + geom_point() + scale_fill_viridis_c()
-```
-
-You can turn off the default filling by setting `filling = FALSE`
-```{r}
-ggheat(small_mat, filling = FALSE) +
- scale_fill_viridis_c() +
- geom_text(aes(label = sprintf("%d * %d", .row_index, .column_index)))
-```
-
-Heatmap annotation works by adding additional information for heatmap
-rows/columns. Heatmap annotations can be positioned at the `top`, `left`,
-`bottom`, or `right` of the heatmap. This is referred to as the active context
-in `ggheat`.
-
->`ggheat` offers two primary annotations: `htanno` and `gganno`.
-
-## `htanno`
-
-`htanno` is a special annotation that can interact with the main heatmap. It
-particularly allows for controlling the order of the main heatmap or dividing
-the heatmap into sections based on rows/columns. Some of them can also adding
-plot.
-
-Currently, there are four sub-classes of `htanno`: `htanno_group`,
-`htanno_reorder`, `htanno_kmeans` and `htanno_dendro`.
-
-### `htanno_group`
-
-`htanno_group` just group heatmap rows/columns into different panels.
-
-By default, the `ggheat` function does not initialize any active context, so if
-you want to add annotations, you need to specify the `position` argument. We can
-omit it if there is any active context in the heatmap (we'll introduce how to
-set the active context after for details).
-```{r htanno_group_top}
-ggheat(small_mat) +
- htanno_group(
- sample(letters[1:4], ncol(small_mat), replace = TRUE),
- position = "top"
- )
-```
-
-```{r htanno_group_left}
-ggheat(small_mat) +
- htanno_group(
- sample(letters[1:4], nrow(small_mat), replace = TRUE),
- position = "left"
- )
-```
-
-### `htanno_reorder`
-`htanno_reorder` reorder heatmap rows/columns based on a summary function.
-```{r}
-ggheat(small_mat) + htanno_reorder(rowMeans, position = "left")
-```
-
-Some annotation function includes a `data` argument to specify the annotation
-data. This argument can accept a matrix, a data frame, or even a simple vector
-that will be converted into a one-column matrix. If the `data` argument is set
-to `NULL`, the function will use the heatmap matrix, as shown in the previous
-example. Additionally, the `data` argument can also accept a function (purrr-like
-lambda is also okay), which will be applied with the heatmap matrix.
-
-> It is important to note that all annotations consider the rows as the
-> observations. It means the `NROW` function must return the same number as the
-> heatmap parallel axis. So for column annotation, the heatmap will be transposed
-> before using (If `data` is a function, it will be applied with the transposed
-> matrix).
-
-So even for top and bottom annotation, we can also use the `rowMeans` to calculate
-the mean value for all columns.
-
-```{r}
-ggheat(small_mat) + htanno_reorder(rowMeans, position = "top")
-```
-
-### `htanno_kmeans`
-`htanno_kmeans` group heatmap rows/columns by kmeans.
-```{r}
-ggheat(small_mat) + htanno_kmeans(3L, position = "t")
-```
-
-It is important to note that both `htanno_group` and `htanno_kmeans` cannot do
-sub-groups. It means when there has been any groups exist. You cannot use them
-
-```{r error=TRUE}
-ggheat(small_mat) +
- htanno_group(
- sample(letters[1:4], ncol(small_mat), replace = TRUE),
- position = "t"
- ) +
- htanno_kmeans(3L)
-```
-
-```{r error=TRUE}
-ggheat(small_mat) +
- htanno_kmeans(3L, position = "t") +
- htanno_group(sample(letters[1:4], ncol(small_mat), replace = TRUE))
-```
-
-You may have noticed that the `htanno_group` function does not explicitly set
-the `position` argument after `htanno_kmeans`. When adding an annotation, we can
-set the active context using the `set_context` argument. This argument requires
-a boolean value of length `2`. It will be recycled for a single value.
-
- - The first value determines whether the active context is set to
- the annotation `position`.
- - The second value will determine whether the active context of the annotation
- list in this position should be set as current annotation.
-
-In the case of `htanno_kmeans`, the default `set_context` value is `c(TRUE,
-FALSE)`, implying that the active context is already set by `htanno_kmeans`.
-
-### htanno_dendro
-`htanno_dendro` class the addition of a dendrogram near the heatmap and and it
-can also reorder the heatmap. This is primarily useful when working with
-heatmap plots.
-
-```{r}
-ggheat(small_mat) + htanno_dendro(position = "top")
-```
-
-You can use the `distance` and `method` argument to control the dendrogram
-builind proce.
-
-```{r}
-ggheat(small_mat) + htanno_dendro(position = "top", method = "ward.D2")
-```
-
-One useful function of dendrogram is to cut the columns/rows into groups. You
-can specify `k` or `h`, which works the same with `cutree`.
-
-```{r}
-ggheat(small_mat) + htanno_dendro(position = "top", k = 3)
-```
-
-In contrast to `htanno_group`, `htanno_kmeans`, and `htanno_reorder`,
-`htanno_dendro` is capable of drawing plot components. Therefore, it has a
-default `set_context` value of `c(TRUE, TRUE)`, we can directly add ggplot
-elements after `htanno_dendro` function.
-
-```{r}
-ggheat(small_mat) +
- htanno_dendro(position = "top") +
- geom_point(aes(y = y))
-```
-
-`htanno_dendro` will create a default `node` data for the ggplot. See
-`?dendrogram_data` for details. In addition, `edge` data has been added into the
-`geom_segment` layer directly which was used to draw the dendrogram tree. One
-useful variable in both `node` and edge `data` is `branch` column, which
-corresponding to the `cutree` result.
-
-```{r}
-ggheat(small_mat) +
- htanno_dendro(aes(color = branch), position = "top", k = 3) +
- geom_point(aes(color = branch, y = y))
-```
-
-`htanno_dendro` is also capable of performing clustering between groups. This
-means that you can use it even if there are already existing groups present in
-the heatmap.
-
-```{r}
-column_groups <- sample(letters[1:3], ncol(small_mat), replace = TRUE)
-ggheat(small_mat) +
- htanno_group(column_groups, "t") +
- htanno_dendro(aes(color = branch))
-```
-
-You can reorder the groups by setting `reorder_group = TRUE`.
-```{r}
-ggheat(small_mat) +
- htanno_group(column_groups, "t") +
- htanno_dendro(aes(color = branch), reorder_group = TRUE)
-```
-
-You can see the difference.
-```{r}
-ggheat(small_mat) +
- htanno_group(column_groups, "t") +
- htanno_dendro(aes(color = branch), reorder_group = TRUE) +
- htanno_dendro(aes(color = branch), reorder_group = FALSE, position = "b")
-```
-
-It is important to understand that when `reorder_group = FALSE` is used, the
-reordering of the heatmap occurs within each group. As long as the ordering
-within each group remains the same, these two dendrograms can be placed on the
-same axis of the heatmap. This is why adding a dendrogram with` reorder_group =
-FALSE` behind a dendrogram with `reorder_group = TRUE` is acceptable, as the
-second `htanno_dendro` will follow the group ordering established by the first
-one. However, it is not possible to add a dendrogram with `reorder_group = TRUE`
-behind a dendrogram with `reorder_group = FALSE` because the second dendrogram
-would not be able to conform to the grouping order followed by the first
-dendrogram.
-
-```{r error=TRUE}
-ggheat(small_mat) +
- htanno_group(column_groups, "t") +
- htanno_dendro(aes(color = branch), reorder_group = FALSE) +
- htanno_dendro(aes(color = branch), reorder_group = TRUE, position = "b")
-```
-
->`ggheat` always prevent user from reordering the heatmap twice.
-
-## `gganno`
-
-`gganno` is similar to `ggheat` and `ggplot` in that it initializes a `ggplot`
-data and `mapping`. The data input can be a matrix, a data frame, or a simple
-vector that will be converted into a one-column matrix, and can inherit from the
-heatmap matrix. But for ggplot usage, matrix (including a simple vector) data is
-converted into a long-format data frame, similar to the process utilized in
-`ggheat`. But note that the long-format data frame does not contain `.row_panel`
-or `.column_panel` column, as annotations can only have one facet axis. In the
-case where the input data is already a data frame, three additional
-columns-`.row_names`, `.row_index`, and `.panel`—are added to the data frame.
-
-Let's add more annotations to different position. Since we want to add
-annotation into another position, we must specify the `position` argument or we
-can add an `active` object (we also provide `activate` and `deactivate`
-for function call foramt).
-
-For convenient, we also provide `gganno_*` function for 4 positions.
-
-```{r}
-ggheat(small_mat) +
- scale_fill_viridis_c(guide = "none") +
- htanno_dendro(aes(color = branch), position = "top", k = 3) +
- gganno(data = rowSums) +
- geom_bar(aes(y = value, fill = .panel), stat = "identity") +
- scale_fill_brewer(palette = "Dark2") +
- gganno_left(aes(x = value), data = rowSums) +
- geom_bar(
- aes(y = .y, fill = factor(.y)),
- stat = "identity",
- orientation = "y"
- ) +
- scale_fill_brewer(palette = "Set1", guide = "none") +
- scale_x_reverse()
-```
-
-## Control size
-The different ggplot objects were combined using the `patchwork` package.
-Internally, the `ggheat_build` function was used to construct and merge all the
-`ggplot` objects into a single `patchwork` object.
-
-`ggheat` has `width` and `height` to control the relative (you can also provide
-a unit object) width and height. All annotation function have a `size` argument
-to control the relative width (left and right annotation) or height (top and
-bottom annotation).
-
-```{r}
-ggheat(small_mat) +
- scale_fill_viridis_c() +
- gganno_top(data = rowSums, size = unit(10, "mm")) +
- geom_bar(aes(y = value, fill = .x), stat = "identity") +
- gganno_left(aes(x = value), data = rowSums, size = 0.5) +
- geom_bar(
- aes(y = .y, fill = factor(.y)),
- stat = "identity",
- orientation = "y"
- ) +
- scale_fill_brewer(palette = "Set1", guide = "none") +
- scale_x_reverse()
-```
-
-## active
-An alternative method to modify the active context is by adding an `active`
-object.
-
-```{r active_top}
-ggheat(small_mat) +
- active("top") +
- htanno_group(sample(letters[1:4], ncol(small_mat), replace = TRUE))
-```
-
-```{r active_null}
-ggheat(small_mat) +
- active("top") +
- htanno_dendro(aes(color = branch), k = 3) +
- ylab("I'm top annotation") +
- active(NULL) +
- ylab("I'm the main heatmap")
-```
-
-## restriction
-The position scales and facets are partial support.
-
-For position scales, you cannot set `limits`, `breaks`, `labels`, and they are
-just ignored. `limits` cannot be touched, and the internal will always reset it
-as the default. This is required to match the heatmap and annotation limits. But
-you can set `labels` or `breaks` in `ggheat()` function. See `xlabels/ylabels`
-and `xlabels_nudge/ylabels_nudge`. All of these arguments should be provided in
-the original order of the raw matrix. Even if we use heatmap annotation to
-reorder the heatmap rows/columns.
-```{r}
-ggheat(small_mat) + scale_x_continuous(limits = c(0, 0))
-```
-
-```{r}
-ggheat(small_mat) + scale_x_continuous(labels = "a")
-```
-
-```{r}
-ggheat(small_mat, xlabels = rep_len("AA", ncol(small_mat)))
-```
-
-When working with facets, manual configuration of panels using the `facet_*`
-function is not possible since the internal will use `facet_grid` to set the
-row/column groups controlled by heatmap annotation. However, you can also
-provide `facet_grid` or `facet_null` (if no panels) to control the non-layout
-arguments, like `labeller`.
-
-```{r}
-ggheat(small_mat) +
- facet_grid(labeller = labeller(.panel = function(x) letters[as.integer(x)])) +
- htanno_dendro(aes(color = branch), position = "top", k = 3) +
- geom_point(aes(y = y))
-```
-
-## Session information
-```{r}
-sessionInfo()
-```
diff --git a/README.html b/README.html
index e7301978..d289792a 100644
--- a/README.html
+++ b/README.html
@@ -603,416 +603,10 @@
-ggheat
-
-
-
-
-
-This package is a ggplot2 extension for heatmap. It
-utilizes the grammar of graphics to construct the heatmap and heatmap
-annotations.
Installation
You can install the development version of ggheat from GitHub with:
# install.packages("devtools")
pak::pkg_install("Yunuuuu/ggheat")
library(ggheat)
-#> Loading required package: ggplot2
Let’s begin by creating some example data
-set.seed(123)
-small_mat <- matrix(rnorm(81), nrow = 9)
-rownames(small_mat) <- paste0("row", seq_len(nrow(small_mat)))
-colnames(small_mat) <- paste0("column", seq_len(ncol(small_mat)))
ggheat
-The core function in the ggheat package is
-ggheat, which sets the default data and mapping for the
-heatmap. Creating a simple heatmap is effortless with the
-ggheat function
-
-
-
-The data can be a numeric or character vector, a data frame, and any
-other data which can be converted into a matrix. Simple vector will be
-converted into a one column matrix. They will all converted into the
-long formated data frame when drawing. The default mapping will use
-aes(.data$.x, .data$.y), but can be controlled using
-mapping argument. The data in the underlying ggplot object
-contains following columns:
-
-.row_panel or .column_panl instead of a
-column .panel since annotation can only have one facet
-axiss: the row panel
.column_panel: the column panel
.row_names and .column_names: the row
-and column names of the original matrix (only applicable when names
-exist).
.row_index and .column_index: the row
-and column index of the original matrix.
.x and .y: the x and
-y coordinates
value: the actual matrix value.
-
-
-
-
-
-
-You can then add all other ggplot2 elements like geoms,
-scales and facets.
-ggheat(small_mat) + geom_point() + scale_fill_viridis_c()
-
-You can turn off the default filling by setting
-filling = FALSE
-ggheat(small_mat, filling = FALSE) +
- scale_fill_viridis_c() +
- geom_text(aes(label = sprintf("%d * %d", .row_index, .column_index)))
-
-Heatmap annotation works by adding additional information for heatmap
-rows/columns. Heatmap annotations can be positioned at the
-top, left, bottom, or
-right of the heatmap. This is referred to as the active
-context in ggheat.
-
-ggheat offers two primary annotations:
-htanno and gganno.
-
-htanno
-htanno is a special annotation that can interact with
-the main heatmap. It particularly allows for controlling the order of
-the main heatmap or dividing the heatmap into sections based on
-rows/columns. Some of them can also adding plot.
-Currently, there are four sub-classes of htanno:
-htanno_group, htanno_reorder,
-htanno_kmeans and htanno_dendro.
-htanno_group
-htanno_group just group heatmap rows/columns into
-different panels.
-By default, the ggheat function does not initialize any
-active context, so if you want to add annotations, you need to specify
-the position argument. We can omit it if there is any
-active context in the heatmap (we’ll introduce how to set the active
-context after for details).
-ggheat(small_mat) +
- htanno_group(
- sample(letters[1:4], ncol(small_mat), replace = TRUE),
- position = "top"
- )
-
-ggheat(small_mat) +
- htanno_group(
- sample(letters[1:4], nrow(small_mat), replace = TRUE),
- position = "left"
- )
-
-htanno_reorder
-htanno_reorder reorder heatmap rows/columns based on a
-summary function.
-ggheat(small_mat) + htanno_reorder(rowMeans, position = "left")
-
-Some annotation function includes a data argument to
-specify the annotation data. This argument can accept a matrix, a data
-frame, or even a simple vector that will be converted into a one-column
-matrix. If the data argument is set to NULL,
-the function will use the heatmap matrix, as shown in the previous
-example. Additionally, the data argument can also accept a
-function (purrr-like lambda is also okay), which will be applied with
-the heatmap matrix.
-
-It is important to note that all annotations consider the rows as the
-observations. It means the NROW function must return the
-same number as the heatmap parallel axis. So for column annotation, the
-heatmap will be transposed before using (If data is a
-function, it will be applied with the transposed matrix).
-
-So even for top and bottom annotation, we can also use the
-rowMeans to calculate the mean value for all columns.
-ggheat(small_mat) + htanno_reorder(rowMeans, position = "top")
-
-htanno_kmeans
-htanno_kmeans group heatmap rows/columns by kmeans.
-ggheat(small_mat) + htanno_kmeans(3L, position = "t")
-
-It is important to note that both htanno_group and
-htanno_kmeans cannot do sub-groups. It means when there has
-been any groups exist. You cannot use them
-ggheat(small_mat) +
- htanno_group(
- sample(letters[1:4], ncol(small_mat), replace = TRUE),
- position = "t"
- ) +
- htanno_kmeans(3L)
-#> Error in `htanno_kmeans()`:
-#> ! `htann_kmeans()` cannot do sub-split
-#> ℹ group of heatmap column already exists
ggheat(small_mat) +
- htanno_kmeans(3L, position = "t") +
- htanno_group(sample(letters[1:4], ncol(small_mat), replace = TRUE))
-#> Error in `htanno_group()`:
-#> ! `htanno_group()` cannot do sub-split
-#> ℹ group of heatmap column already exists
You may have noticed that the htanno_group function does
-not explicitly set the position argument after
-htanno_kmeans. When adding an annotation, we can set the
-active context using the set_context argument. This
-argument requires a boolean value of length 2. It will be
-recycled for a single value.
-
-- The first value determines whether the active context is set to the
-annotation
position.
-- The second value will determine whether the active context of the
-annotation list in this position should be set as current
-annotation.
-
-In the case of htanno_kmeans, the default
-set_context value is c(TRUE, FALSE), implying
-that the active context is already set by
-htanno_kmeans.
-htanno_dendro
-htanno_dendro class the addition of a dendrogram near
-the heatmap and and it can also reorder the heatmap. This is primarily
-useful when working with heatmap plots.
-ggheat(small_mat) + htanno_dendro(position = "top")
-
-You can use the distance and method
-argument to control the dendrogram builind proce.
-ggheat(small_mat) + htanno_dendro(position = "top", method = "ward.D2")
-
-One useful function of dendrogram is to cut the columns/rows into
-groups. You can specify k or h, which works
-the same with cutree.
-ggheat(small_mat) + htanno_dendro(position = "top", k = 3)
-
-In contrast to htanno_group, htanno_kmeans,
-and htanno_reorder, htanno_dendro is capable
-of drawing plot components. Therefore, it has a default
-set_context value of c(TRUE, TRUE), we can
-directly add ggplot elements after htanno_dendro
-function.
-ggheat(small_mat) +
- htanno_dendro(position = "top") +
- geom_point(aes(y = y))
-
-htanno_dendro will create a default node
-data for the ggplot. See ?dendrogram_data for details. In
-addition, edge data has been added into the
-geom_segment layer directly which was used to draw the
-dendrogram tree. One useful variable in both node and edge
-data is branch column, which corresponding to
-the cutree result.
-ggheat(small_mat) +
- htanno_dendro(aes(color = branch), position = "top", k = 3) +
- geom_point(aes(color = branch, y = y))
-
-htanno_dendro is also capable of performing clustering
-between groups. This means that you can use it even if there are already
-existing groups present in the heatmap.
-column_groups <- sample(letters[1:3], ncol(small_mat), replace = TRUE)
-ggheat(small_mat) +
- htanno_group(column_groups, "t") +
- htanno_dendro(aes(color = branch))
-
-You can reorder the groups by setting
-reorder_group = TRUE.
-ggheat(small_mat) +
- htanno_group(column_groups, "t") +
- htanno_dendro(aes(color = branch), reorder_group = TRUE)
-
-You can see the difference.
-ggheat(small_mat) +
- htanno_group(column_groups, "t") +
- htanno_dendro(aes(color = branch), reorder_group = TRUE) +
- htanno_dendro(aes(color = branch), reorder_group = FALSE, position = "b")
-
-It is important to understand that when
-reorder_group = FALSE is used, the reordering of the
-heatmap occurs within each group. As long as the ordering within each
-group remains the same, these two dendrograms can be placed on the same
-axis of the heatmap. This is why adding a dendrogram
-withreorder_group = FALSE behind a dendrogram with
-reorder_group = TRUE is acceptable, as the second
-htanno_dendro will follow the group ordering established by
-the first one. However, it is not possible to add a dendrogram with
-reorder_group = TRUE behind a dendrogram with
-reorder_group = FALSE because the second dendrogram would
-not be able to conform to the grouping order followed by the first
-dendrogram.
-ggheat(small_mat) +
- htanno_group(column_groups, "t") +
- htanno_dendro(aes(color = branch), reorder_group = FALSE) +
- htanno_dendro(aes(color = branch), reorder_group = TRUE, position = "b")
-#> Error in `htanno_dendro()`:
-#> ! `htanno_dendro()` disrupt the previously established order of the
-#> heatmap column
-ggheat always prevent user from reordering the heatmap
-twice.
-
-gganno
-gganno is similar to ggheat and
-ggplot in that it initializes a ggplot data
-and mapping. The data input can be a matrix, a data frame,
-or a simple vector that will be converted into a one-column matrix, and
-can inherit from the heatmap matrix. But for ggplot usage, matrix
-(including a simple vector) data is converted into a long-format data
-frame, similar to the process utilized in ggheat. But note
-that the long-format data frame does not contain .row_panel
-or .column_panel column, as annotations can only have one
-facet axis. In the case where the input data is already a data frame,
-three additional columns-.row_names,
-.row_index, and .panel—are added to the data
-frame.
-Let’s add more annotations to different position. Since we want to
-add annotation into another position, we must specify the
-position argument or we can add an active
-object (we also provide activate and
-deactivate for function call foramt).
-For convenient, we also provide gganno_* function for 4
-positions.
-ggheat(small_mat) +
- scale_fill_viridis_c(guide = "none") +
- htanno_dendro(aes(color = branch), position = "top", k = 3) +
- gganno(data = rowSums) +
- geom_bar(aes(y = value, fill = .panel), stat = "identity") +
- scale_fill_brewer(palette = "Dark2") +
- gganno_left(aes(x = value), data = rowSums) +
- geom_bar(
- aes(y = .y, fill = factor(.y)),
- stat = "identity",
- orientation = "y"
- ) +
- scale_fill_brewer(palette = "Set1", guide = "none") +
- scale_x_reverse()
-
-Control size
-The different ggplot objects were combined using the
-patchwork package. Internally, the
-ggheat_build function was used to construct and merge all
-the ggplot objects into a single patchwork
-object.
-ggheat has width and height to
-control the relative (you can also provide a unit object) width and
-height. All annotation function have a size argument to
-control the relative width (left and right annotation) or height (top
-and bottom annotation).
-ggheat(small_mat) +
- scale_fill_viridis_c() +
- gganno_top(data = rowSums, size = unit(10, "mm")) +
- geom_bar(aes(y = value, fill = .x), stat = "identity") +
- gganno_left(aes(x = value), data = rowSums, size = 0.5) +
- geom_bar(
- aes(y = .y, fill = factor(.y)),
- stat = "identity",
- orientation = "y"
- ) +
- scale_fill_brewer(palette = "Set1", guide = "none") +
- scale_x_reverse()
-
-active
-An alternative method to modify the active context is by adding an
-active object.
-ggheat(small_mat) +
- active("top") +
- htanno_group(sample(letters[1:4], ncol(small_mat), replace = TRUE))
-
-ggheat(small_mat) +
- active("top") +
- htanno_dendro(aes(color = branch), k = 3) +
- ylab("I'm top annotation") +
- active(NULL) +
- ylab("I'm the main heatmap")
-
-restriction
-The position scales and facets are partial support.
-For position scales, you cannot set limits,
-breaks, labels, and they are just ignored.
-limits cannot be touched, and the internal will always
-reset it as the default. This is required to match the heatmap and
-annotation limits. But you can set labels or
-breaks in ggheat() function. See
-xlabels/ylabels and
-xlabels_nudge/ylabels_nudge. All of these arguments should
-be provided in the original order of the raw matrix. Even if we use
-heatmap annotation to reorder the heatmap rows/columns.
-ggheat(small_mat) + scale_x_continuous(limits = c(0, 0))
-#> Scale for x is already present.
-#> Adding another scale for x, which will replace the existing scale.
ggheat(small_mat) + scale_x_continuous(labels = "a")
-#> Scale for x is already present.
-#> Adding another scale for x, which will replace the existing scale.
ggheat(small_mat, xlabels = rep_len("AA", ncol(small_mat)))
-
-When working with facets, manual configuration of panels using the
-facet_* function is not possible since the internal will
-use facet_grid to set the row/column groups controlled by
-heatmap annotation. However, you can also provide
-facet_grid or facet_null (if no panels) to
-control the non-layout arguments, like labeller.
-ggheat(small_mat) +
- facet_grid(labeller = labeller(.panel = function(x) letters[as.integer(x)])) +
- htanno_dendro(aes(color = branch), position = "top", k = 3) +
- geom_point(aes(y = y))
sessionInfo()
-#> R version 4.4.0 (2024-04-24)
-#> Platform: x86_64-pc-linux-gnu
-#> Running under: Ubuntu 24.04 LTS
-#>
-#> Matrix products: default
-#> BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libmkl_rt.so; LAPACK version 3.8.0
-#>
-#> locale:
-#> [1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
-#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
-#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
-#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
-#>
-#> time zone: Asia/Shanghai
-#> tzcode source: system (glibc)
-#>
-#> attached base packages:
-#> [1] stats graphics grDevices utils datasets methods base
-#>
-#> other attached packages:
-#> [1] ggheat_0.0.1 ggplot2_3.5.1
-#>
-#> loaded via a namespace (and not attached):
-#> [1] gtable_0.3.5 dplyr_1.1.4 compiler_4.4.0 highr_0.11
-#> [5] tidyselect_1.2.1 tidyr_1.3.1 scales_1.3.0 yaml_2.3.8
-#> [9] fastmap_1.2.0 ggh4x_0.2.8 R6_2.5.1 labeling_0.4.3
-#> [13] generics_0.1.3 patchwork_1.2.0 knitr_1.47 tibble_3.2.1
-#> [17] munsell_0.5.1 pillar_1.9.0 RColorBrewer_1.1-3 rlang_1.1.4
-#> [21] utf8_1.2.4 xfun_0.45 viridisLite_0.4.2 cli_3.6.3
-#> [25] withr_3.0.0 magrittr_2.0.3 digest_0.6.36 grid_4.4.0
-#> [29] lifecycle_1.0.4 vctrs_0.6.5 evaluate_0.24.0 glue_1.7.0
-#> [33] farver_2.1.2 fansi_1.0.6 colorspace_2.1-0 rmarkdown_2.27
-#> [37] purrr_1.0.2 tools_4.4.0 pkgconfig_2.0.3 htmltools_0.5.8.1