visCluster: using visCluster to visualize cluster results from...

In ClusterGVis: One-Step to Cluster and Visualize Gene Expression Data

using visCluster to visualize cluster results from clusterData and enrichCluster output

Description

Visualize Clustered Gene Data Using Line Plots and Heatmaps

Usage

visCluster(
  object = NULL,
  ht.col.list = list(col_range = c(-2, 0, 2), col_color = c("#08519C", "white",
    "#A50F15")),
  border = TRUE,
  plot.type = c("line", "heatmap", "both"),
  ms.col = c("#0099CC", "grey90", "#CC3333"),
  line.size = 0.1,
  line.col = "grey90",
  add.mline = TRUE,
  mline.size = 2,
  mline.col = "#CC3333",
  ncol = 4,
  ctAnno.col = NULL,
  set.md = "median",
  textbox.pos = c(0.5, 0.8),
  textbox.size = 8,
  panel.arg = c(2, 0.25, 4, "grey90", NA),
  ggplot.panel.arg = c(2, 0.25, 4, "grey90", NA),
  annoTerm.data = NULL,
  annoTerm.mside = "right",
  termAnno.arg = c("grey95", "grey50"),
  add.bar = FALSE,
  bar.width = 8,
  textbar.pos = c(0.8, 0.8),
  go.col = NULL,
  go.size = NULL,
  by.go = "anno_link",
  annoKegg.data = NULL,
  annoKegg.mside = "right",
  keggAnno.arg = c("grey95", "grey50"),
  add.kegg.bar = FALSE,
  kegg.col = NULL,
  kegg.size = NULL,
  by.kegg = "anno_link",
  word_wrap = TRUE,
  add_new_line = TRUE,
  add.box = FALSE,
  boxcol = NULL,
  box.arg = c(0.1, "grey50"),
  add.point = FALSE,
  point.arg = c(19, "orange", "orange", 1),
  add.line = TRUE,
  line.side = "right",
  markGenes = NULL,
  markGenes.side = "right",
  genes.gp = c("italic", 10, NA),
  term.text.limit = c(10, 18),
  mulGroup = NULL,
  lgd.label = NULL,
  show_row_names = FALSE,
  subgroup.anno = NULL,
  annnoblock.text = TRUE,
  annnoblock.gp = c("white", 8),
  add.sampleanno = TRUE,
  sample.group = NULL,
  sample.col = NULL,
  sample.order = NULL,
  cluster.order = NULL,
  sample.cell.order = NULL,
  HeatmapAnnotation = NULL,
  column.split = NULL,
  cluster_columns = FALSE,
  pseudotime_col = NULL,
  gglist = NULL,
  row_annotation_obj = NULL,
  ...
)

Arguments

object	clusterData object, default NULL.
ht.col.list	list of heatmap col_range and col_color, default list(col_range = c(-2, 0, 2),col_color = c("#08519C", "white", "#A50F15")).
border	whether add border for heatmap, default TRUE.
plot.type	the plot type to choose which incuding "line","heatmap" and "both".
ms.col	membership line color form Mfuzz cluster method results, default c('#0099CC','grey90','#CC3333').
line.size	line size for line plot, default 0.1.
line.col	line color for line plot, default "grey90".
add.mline	whether add median line on plot, default TRUE.
mline.size	median line size, default 2.
mline.col	median line color, default "#CC3333".
ncol	the columns for facet plot with line plot, default 4.
ctAnno.col	the heatmap cluster annotation bar colors, default NULL.
set.md	the represent line method on heatmap-line plot(mean/median), default "median".
textbox.pos	the relative position of text in left-line plot, default c(0.5,0.8).
textbox.size	the text size of the text in left-line plot, default 8.
panel.arg	the settings for the left-line panel which are panel size,gap,width,fill and col, default c(2,0.25,4,"grey90",NA).
ggplot.panel.arg	the settings for the ggplot2 object plot panel which are panel size,gap,width,fill and col, default c(2,0.25,4,"grey90",NA).
annoTerm.data	the GO term annotation for the clusters, default NULL.
annoTerm.mside	the wider GO term annotation box side, default "right".
termAnno.arg	the settings for GO term panel annotations which are fill and col, default c("grey95","grey50").
add.bar	whether add bar plot for GO enrichment, default FALSE.
bar.width	the GO enrichment bar width, default 8.
textbar.pos	the barplot text relative position, default c(0.8,0.8).
go.col	the GO term text colors, default NULL.
go.size	the GO term text size(numeric or "pval"), default NULL.
by.go	the GO term text box style("anno_link" or "anno_block"), default "anno_link".
annoKegg.data	the KEGG term annotation for the clusters, default NULL.
annoKegg.mside	the wider KEGG term annotation box side, default "right".
keggAnno.arg	the settings for KEGG term panel annotations which are fill and col, default c("grey95","grey50").
add.kegg.bar	whether add bar plot for KEGG enrichment, default FALSE.
kegg.col	the KEGG term text colors, default NULL.
kegg.size	the KEGG term text size(numeric or "pval"), default NULL.
by.kegg	the KEGG term text box style("anno_link" or "anno_block"), default "anno_link".
word_wrap	whether wrap the text, default TRUE.
add_new_line	whether add new line when text is long, default TRUE.
add.box	whether add boxplot, default FALSE.
boxcol	the box fill colors, default NULL.
box.arg	this is related to boxplot width and border color, default c(0.1,"grey50").
add.point	whether add point, default FALSE.
point.arg	this is related to point shape,fill,color and size, default c(19,"orange","orange",1).
add.line	whether add line, default TRUE.
line.side	the line annotation side, default "right".
markGenes	the gene names to be added on plot, default NULL.
markGenes.side	the gene label side, default "right".
genes.gp	gene labels graphics settings, default c('italic',10,NA).
term.text.limit	the GO term text size limit, default c(10,18).
mulGroup	to draw multiple lines annotation, supply the groups numbers with vector, default NULL.
lgd.label	the lines annotation legend labels, default NULL.
show_row_names	whether to show row names, default FALSE.
subgroup.anno	the sub-cluster for annotation, supply sub-cluster id, default NULL.
annnoblock.text	whether add cluster numbers on right block annotation, default TRUE.
annnoblock.gp	right block annotation text color and size, default c("white",8).
add.sampleanno	whether add column annotation, default TRUE.
sample.group	the column sample groups, default NULL.
sample.col	column annotation colors, default NULL.
sample.order	the orders for column samples, default NULL.
cluster.order	the row cluster orders for user's own defination, default NULL.
sample.cell.order	the celltype order when input is scRNA data and "showAverage = FALSE" for prepareDataFromscRNA.
HeatmapAnnotation	the 'HeatmapAnnotation' object from 'ComplexHeatmap' when you have multiple annotations, default NULL.
column.split	how to split the columns when supply multiple column annotations, default NULL.
cluster_columns	whether cluster the columns, default FALSE.
pseudotime_col	the branch color control for monocle input data.
gglist	a list of ggplot object to annotate each cluster, default NULL.
row_annotation_obj	Row annotation for heatmap, it is a ComplexHeatmap::rowAnnotation() object when "markGenes.side" or ”line.side“ is "right". Otherwise is a list of named vectors.
...	othe aruguments passed by Heatmap fuction.

Details

This function visualizes clustered gene expression data as line plots, heatmaps, or a combination of both, using the ComplexHeatmap and ggplot2 frameworks. Gene annotations, sample annotations, and additional features like custom color schemes and annotations for GO/KEGG terms are supported for visualization.

Value

a ggplot2 or Heatmap object.

Author(s)

JunZhang

Examples

data("exps")

# mfuzz
cm <- clusterData(obj = exps,
                  cluster.method = "kmeans",
                  cluster.num = 8)

# plot
visCluster(object = cm,
           plot.type = "line")

ClusterGVis documentation built on April 4, 2025, 2:27 a.m.