peakCMeans(matrix,
nsize = "3,3",
threshold = 10,
fuzzification = 2,
plotSize = "8100,5200",
colorSet = "Jet",
memberCutoff = 0.8,
empty.shared = 2,
max.cluster.shared = 3,
xlab = "Spatial Regions",
ylab = "z-score(Normalized Intensity)",
top.members = 0.2,
margin = "padding:100px 100px 300px 100px;",
cluster.label.css = "font-style: normal; font-size: 20; font-family: Bookman Old Style;",
legend.title.css = "font-style: normal; font-size: 10; font-family: Microsoft YaHei;",
legend.tick.css = "font-style: normal; font-size: 10; font-family: Microsoft YaHei;",
axis.tick.css = "font-style: normal; font-size: 12; font-family: Segoe UI;",
axis.label.css = "font-style: normal; font-size: 10; font-family: Microsoft YaHei;",
grid.fill = "LightGray",
grid.draw = TRUE,
x.lab.rotate = 45);
matrix
A gene expression data matrix object. [as Matrix]
nsize
the layout of the cmeans clustering visualization
threshold
the cmeans threshold. [as double]
plotSize
the image size of the cmeans plot
colorSet
the color palatte name. [as string]
fuzzification
cmeans fuzzification parameter. [as double]
memberCutoff
the cmeans membership cutoff value for create a molecule cluster. [as double]
empty.shared
how many clusters will be assigned to a gene feature when there is no cluster that its membership value is greater than the memberCutoff threshold. [as integer]
max.cluster.shared
the max cluster numbers that a gene feature can be assigned into. [as integer]
xlab
the x axis label text of the cmeans pattern plot. [as string]
ylab
the y axis label text of the cmeans pattern plot. [as string]
top.members
the ratio of the top members of each cluster for draw the expression pattern lines in the cmeans pattern plot. [as double]
margin
the plot padding css style of the cmeans pattern plot.
cluster.label.css
the css style of the cluster label text. [as string]
legend.title.css
the css style of the legend title text. [as string]
legend.tick.css
the css style of the legend tick text. [as string]
axis.tick.css
the css style of the axis tick text. [as string]
axis.label.css
the css style of the axis label text. [as string]
grid.fill
the background fill color of the plot grid. [as string]
grid.draw
draw the plot grid lines or not?. [as boolean]
x.lab.rotate
the rotate angle of the x axis label text. [as double]
env
the R# runtime environment object. [as Environment]
this function returns a tuple list that contains the pattern cluster matrix and the cmeans pattern plots.
NULL will be returns if the given expression matrix is empty.