plotRadar {LipidomicsR}

plotRadar()

Description

A function to produce radar plot based on lipid types, carbon number, and number of double bonds.

Usage

plotRadar(
  data,
  pattern,
  group,
  max = 0.6,
  min = 0,
  method = "median",
  axislabcol = "grey",
  plwd = 2,
  plty = 1,
  cglcol = 1,
  seg = 4,
  cglwd = 1,
  cglty = 3,
  vlcex = 1,
  axistype = 1,
  t.size = 15,
  t.vjust = 0,
  t.color = "black",
  l.postion = "topright",
  l.bty = "n",
  lt.col = "grey25",
  lt.cex = 2,
  l.cex = 1
)

Arguments

data

A dataframe storing absolute concentration or PL to get normalized data. The column name should be the sample name and the row name should be the lipid type. The class of column name and row name should be "character". The class of values should be "numeric". The row names are recommended to be in a form like "PL(14:0/20:1)" or "LPL(16:1)".

pattern

Can accept 4 values: "lipid", "CB", "sat", or "all"

If pattern="lipid“, a new radar diagram based on lipid type will be saved, which was named as "lipid_RadarChart.pdf"

If pattern="CB“, a new radar diagram based on carbon number will be saved, which was named as "carbon_number_RadarChart.pdf"

If pattern="sat“, a new radar diagram based on the number of double bonds will be saved, which was named as "unsaturation_RadarChart.pdf"

If pattern="all“, all three diagrams will be saved.

group

A vector defining which group the replicates belong to. Notice: the number of groups should be less than 17.

max

The maximal absolute concentration or PL% values of each class. The default value is 0.6.

min

The minimal absolute concentration or PL% values of each class. The default value is 0.

method

The method to select the representative value from a group, which can be "median" or "mean". If it equals "median", the median of the group samples will be chosen. Otherwise, the mean will be chosen to plot.

axislabcol

The color of axis, default value is "grey".

plwd

Defines the width of the data series line. Default value is 2.

plty

Specifies the style of the data series line, which can be 1-6. Default value is 1.

cglcol

Specifies the color of the gridlines. Default value is 1.

seg

Defines the number of gridlines. Default value is 4, which means 5 gridlines: "0%", "25%", "50%", "75%", and "100%".

cglwd

Specifies the width of the gridlines. Default value is 1.

cglty

Specifies the grid line style, which can be 1-6. Default value is 3.

vlcex

Specifies the size of the group label font. Default value is 1.

axistype

Specifies the style of the axis, which can be 0-5. Default value is 1.

t.size

The size of picture title. Default value is 15.

t.vjust

The vertical position of picture title, which can be negative or positivew values. Default value is 0.

t.color

The color of picture title. Default value is "black".

l.postion

The position of legend, which can be "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" or "center". Default value is "topright".

l.bty

Whether the legend box is drawn, "o" means drawn, and the default value is "n" not drawn.

lt.col

The color of legend text. Default value is "grey25".

lt.cex

The fontsize of legend text. Default value is 2.

l.cex

The size of legend. Default value is 1.

Value

No return value, called for side effects, which is a radar diagram based on lipid type, carbon number, or unsaturation among different groups.

Examples

WT_1=rnorm(n=10,mean=0.4,sd=0.1)
WT_2=rnorm(n=10,mean=0.4,sd=0.1)
WT_3=rnorm(n=10,mean=0.4,sd=0.1)
WT_4=rnorm(n=10,mean=0.4,sd=0.1)
KO_1=rnorm(n=10,mean=0.8,sd=0.1)
KO_2=rnorm(n=10,mean=0.8,sd=0.1)
KO_3=rnorm(n=10,mean=0.8,sd=0.1)
KO_4=rnorm(n=10,mean=0.8,sd=0.1)
WT_treat_1=rnorm(n=10,mean=0.1,sd=0.1)
WT_treat_2=rnorm(n=10,mean=0.1,sd=0.1)
WT_treat_3=rnorm(n=10,mean=0.1,sd=0.1)
WT_treat_4=rnorm(n=10,mean=0.1,sd=0.1)
KO_treat_1=rnorm(n=10,mean=0.6,sd=0.1)
KO_treat_2=rnorm(n=10,mean=0.6,sd=0.1)
KO_treat_3=rnorm(n=10,mean=0.6,sd=0.1)
KO_treat_4=rnorm(n=10,mean=0.6,sd=0.1)
data=data.frame(WT_1,WT_2,WT_3,WT_4,KO_1,KO_2,KO_3,KO_4,
                WT_treat_1,WT_treat_2,WT_treat_3,WT_treat_4,
                KO_treat_1,KO_treat_2,KO_treat_3,KO_treat_4)
rownames(data)=c("LPC(16:0)","PC(14:0/16:1)","PC(18:1/18:1)","PE(18:0/20:1)",
                 "PS(20:1/20:1)","PI(16:0/16:1)","PC(18:0/18:1)","PA(16:0/16:1)",
                 "LPE(18:0)","PE(O-18:1/18:0)")
group=rep(c("WT","KO","WT_treat","KO_treat"),each=4)
plotRadar(data,"all",group) # This is the most simplified version