Description Usage Arguments Value Author(s) Examples
Plot biomarker or clinical variables properties.
1 2 3 4 5 6 7 8 9 | PlotProperty(data, biomarker.var, biomarker.class = NULL, var = NULL,
var.class = NULL, log2 = FALSE, col = rgb(0, 0, 1, alpha = 0.3),
add.num = 0, text.font = 3, main = "Distribution of", xlab = "",
add.lab = "", border = NULL, add.cor = FALSE, cor.method = "spearman",
lowess.line = FALSE, lowess.line.col = "deepskyblue",
show.biomarker.uni = TRUE, show.clinical.uni = FALSE,
show.association = TRUE, f = 0.3, las = 1, pdf.name = NULL,
pdf.param = list(width = 6, height = 4.5), par.param = list(mar = c(4, 4,
3, 2)), ...)
|
data |
input data frame. Rows are patients and columns are variables (e.g. demographics variables, time to event variables, biomarker variables, treatment indicator, etc.). One patient per row. |
biomarker.var |
name of the biomarker variable. Should be in colnames of |
biomarker.class |
can be either "numeric" or "categorical". If NULL (default), the class will be defined automatically. |
var |
name of a clinical variable. It can be a vector of variables. Should be in colnames of |
var.class |
can be either "numeric" or "categorical". It can be a vector of classes. If NULL (default) and var is not NULL, then |
log2 |
if TRUE, computes binary (i.e. base 2) logarithm. It can be a vector if there are several numeric variables. The |
col |
the color of the line segments or dots. Default is "blue" with 30 percent transparency, i.e. |
add.num |
the constant to add to all values. Helps to avoid applying log transformation on 0 or negative values. Will be ignored if covariate is categorical. Default is 0. |
text.font |
legend text font size. Default is 3. |
main |
the main title. Default is |
xlab |
x axis label. Default is "". |
add.lab |
an additional text to y axis label. Default is "". |
border |
a vector of colors for the outlines of the boxplots. Default is NULL. |
add.cor |
add the correlation coefficient to the boxplot. Default is FALSE. |
cor.method |
which correlation coefficient to compute. One of "pearson", "kendall", or "spearman" (default) can be abbreviated. |
lowess.line |
performs the computations for the |
lowess.line.col |
the smoother color. Default is "deepskyblue". |
show.biomarker.uni, show.clinical.uni, show.association |
indicate whether to show biomarker uni-variate plot, clinical variable uni-variate plot, biomarker-clinical variable association plot, respectively. Default is TRUE for all but show.clinical.uni. |
f |
the smoother span. This gives the proportion of points in the plot which influence the smooth at each value. Larger values give more smoothness. Default is 0.3. |
las |
create a barplot with labels parallel (horizontal) to bars if |
pdf.name |
name of output pdf file. If it's NULL (default), the plots will be displayed but not saved as pdf. |
pdf.param |
a list of parameters that define pdf graphics device. See |
par.param |
a list of parameters that define graphcial parameters. See |
... |
other arguments passed on to the individual functions, like hist(), boxplot(), etc. |
If only a biomarker variable is given, it will crete a density plot for a numeric variable or bar plot for a categorical variable. If only a vactor of clinical variables is provided, it will create a density plot for each numeric variable and a bar plot for each categorical variable. If both a biomarker variable and a vector of clinical variables are given, it will create: a scatter plot for a numeric pair of variables; a bar plot for each categorical variable; a bar plot for a pair of categorical variables; a density plot for a numeric clinical variable; a boxplot for a pair of numeric and categorical variables.
Alexey Pronin pronin.alexey@gene.com, Ning Leng leng.ning@gene.com, and previous team members (see DESCRIPTION)
1 2 3 4 5 6 | data(input)
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric", log2=TRUE)
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric", log2=TRUE, breaks=5)
PlotProperty(data=input, biomarker.var="KRAS.exprs", biomarker.class="numeric", var="OS", var.class="numeric", log2=c(TRUE, FALSE))
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical", var=c("Arm","OS"), var.class=c("categorical", "numeric"), par.param=list(mfrow=c(3, 2)))
PlotProperty(data=input, biomarker.var="KRAS.mutant", biomarker.class="categorical", var=c("Country", "Age"), var.class=c("categorical", "numeric"), col=rgb(0, 0, 1, 0.2), par.param=list(mfrow=c(3,2)))
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