visCluster: 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,
  ...
)

Value

a ggplot2 or Heatmap object.

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.

Author

JunZhang

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.

Examples

Run this code


data("exps")

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

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

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