Usage
"glMDPlot"(x, anno, groups, samples, status = rep(0, nrow(x)), search.by = "Symbols", jitter = 30, id.column = "GeneID", display.columns = id.column, cols = c("#0000FF", "#858585", "#B32222"), sample.cols = rep("#1f77b4", ncol(x)), path = getwd(), folder = "glimma-plots", html = "MD-Plot", launch = TRUE, ...)
Arguments
x
the DESeqDataSet object.
anno
the data.frame containing gene annotations.
groups
the factor containing experimental groups of the samples.
samples
the names of the samples.
status
vector giving the control status of data point, of same length as the number of rows of object. If NULL, then all points are plotted in the default colour.
search.by
the name of the column which will be used to search for data points. (should contain unique values)
jitter
the amount of jitter to apply to the samples in the expressions plot.
id.column
the column containing unique identifiers for each gene.
display.columns
character vector containing names of columns to display in mouseover tooltips.
cols
vector of strings denoting colours corresponding to control status -1, 0 and 1. (may be R named colours or Hex values)
sample.cols
vector of strings denoting colours for each sample point on the expression plot.
path
the path in which the folder will be created.
folder
the name of the fold to save html file to.
html
the name of the html file to save plots to.
launch
TRUE to launch plot after call.
...
additional arguments to be passed onto the MD plot.