Update circos_heatmap function

benben-miao · Jul 26, 2023 · 804c8bf · 804c8bf
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: TOmicsVis
 Type: Package
 Title: Transcriptome Visualization Process Scheme
-Version: 1.2.3
+Version: 1.2.4
 Authors@R: c(
  person(given = "Benben", family = "Miao", email = "[email protected]", 
  role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7307-1331")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,15 @@
+## TOmicsVis 1.2.4
+
+**Date**: 2023-07-26
+
+<span style="background-color: green; border-radius: 10px; padding: 0px 5px; font-weight: bold; color: white;">New Features:</span>
+
+<span style="background-color: red; border-radius: 10px; padding: 0px 5px; font-weight: bold; color: white;">Bugs Fixed:</span>
+
+1. Add new parameters (cluster_run, dend_show, rowname_show) for `?TOmicsVis::circos_heatmap` function.
+
+---
+
 ## TOmicsVis 1.2.3
 
 **Date**: 2023-07-20

diff --git a/R/circos_heatmap.R b/R/circos_heatmap.R
@@ -8,9 +8,12 @@
 #' @param mid_color Character: middle value color (color name or hex value). Default: "#ffffff".
 #' @param high_color Character: high value color (color name or hex value). Default: "#ff0000".
 #' @param gap_size Numeric: heatmap gap size. Default: 10, min: 0.
+#' @param cluster_run Logical: running cluster algorithm. Default: TRUE, options: TRUE, FALSE.
 #' @param cluster_method Character: cluster methods. Default: "complete", options: "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid".
 #' @param distance_method Character: distance methods. Default: "euclidean", options: "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski".
+#' @param dend_show Character: control dendgram display and position. Default: "inside", options: "none", "outside", "inside".
 #' @param dend_height Numeric: dendgram height. Default: 0.20, min: 0.00, max: 0.50.
+#' @param rowname_show Character: control rownames display and position. Hind first rowname by running rownames(data)[1]. Default: "outside", options: "none", "outside", "inside".
 #' @param rowname_size Numeric: rowname font size. Default: 0.80, min: 0.10, max: 10.00.
 #'
 #' @importFrom stats reorder
@@ -35,9 +38,12 @@ circos_heatmap <- function(data,
  mid_color = "#ffffff",
  high_color = "#ff0000",
  gap_size = 10,
+ cluster_run = TRUE,
  cluster_method = "complete",
  distance_method = "euclidean",
+ dend_show = "inside",
  dend_height = 0.20,
+ rowname_show = "outside",
  rowname_size = 0.80
  ){
 
@@ -101,17 +107,18 @@ circos_heatmap <- function(data,
  bg.border = NA,
  bg.lty = graphics::par("lty"),
  bg.lwd = graphics::par("lwd"),
- cluster = TRUE,
+ cluster = cluster_run,
  clustering.method = cluster_method, # "ward.D", "ward.D2", "single", "complete", "average", "mcquitty", "median", "centroid"
  distance.method = distance_method, # "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"
  dend.callback = function(dend, m, si) stats::reorder(dend, rowMeans(m)),
- dend.side = "inside", # "none", "outside", "inside"
+ dend.side = dend_show, # "none", "outside", "inside"
  dend.track.height = dend_height,
- rownames.side = "outside", # "none", "outside", "inside"
+ rownames.side = rowname_show, # "none", "outside", "inside"
  rownames.cex = rowname_size,
  rownames.font = graphics::par("font"),
  rownames.col = "black",
- track.height = 0.3
+ track.height = 0.3,
+ show.sector.labels = FALSE
  )
  # circos.track(track.index = get.current.track.index(),
  # panel.fun = function(x, y) {
@@ -126,7 +133,7 @@ circos_heatmap <- function(data,
  # }, bg.border = NA)
  legend = ComplexHeatmap::Legend(title = "ColorBar", col_fun = col_fun)
  grid::grid.draw(legend)
- circos.clear()
+ circlize::circos.clear()
  }
  # # <- 4. Plot
 

diff --git a/README.Rmd b/README.Rmd
@@ -414,14 +414,17 @@ data(circos_heatmap_data)
 
 # 2. Run circos_heatmap plot function
 circos_heatmap(
- circos_heatmap_data,
+ data = circos_heatmap_data,
  low_color = "#0000ff",
  mid_color = "#ffffff",
  high_color = "#ff0000",
  gap_size = 10,
+ cluster_run = TRUE,
  cluster_method = "complete",
  distance_method = "euclidean",
+ dend_show = "inside",
  dend_height = 0.2,
+ rowname_show = "outside",
  rowname_size = 0.8
 )
 ```

diff --git a/README.md b/README.md
@@ -501,14 +501,17 @@ data(circos_heatmap_data)
 
 # 2. Run circos_heatmap plot function
 circos_heatmap(
- circos_heatmap_data,
+ data = circos_heatmap_data,
  low_color = "#0000ff",
  mid_color = "#ffffff",
  high_color = "#ff0000",
  gap_size = 10,
+ cluster_run = TRUE,
  cluster_method = "complete",
  distance_method = "euclidean",
+ dend_show = "inside",
  dend_height = 0.2,
+ rowname_show = "outside",
  rowname_size = 0.8
 )
 ```

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
diff --git a/docs/LICENSE.html b/docs/LICENSE.html
diff --git a/docs/articles/Tutorials.html b/docs/articles/Tutorials.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.0.7
 pkgdown_sha: ~
 articles:
  Tutorials: Tutorials.html
-last_built: 2023-07-24T09:23Z
+last_built: 2023-07-26T05:08Z
 urls:
  reference: https://github.com/benben-miao/TOmicsVis/reference
  article: https://github.com/benben-miao/TOmicsVis/articles

diff --git a/docs/reference/box_data.html b/docs/reference/box_data.html
diff --git a/docs/reference/box_plot.html b/docs/reference/box_plot.html
diff --git a/docs/reference/chord_data.html b/docs/reference/chord_data.html
diff --git a/docs/reference/chord_plot-2.png b/docs/reference/chord_plot-2.png