Plotting MarkerList Objects

Usage

S3 (MarkerList)
`barplot`(height, data = NULL, col = NULL, byType = TRUE, ylab = NULL, 
  border = missing(data), beside = TRUE, scale = !beside, legend = TRUE, reorder = if (is.null(data)) -1L else FALSE, 
      las = 2, ...)

Arguments

height

a MarkerList-class object.

data

dataset (a matrix or ExpressionSet object) that contains expression values of the markers in some experiment. If not missing, values corresponding to markers are plotted for each column in the data. Markers that do not have corresponding values in data are discarded. Note that no identifier conversion is performed, meaning that the marker list and the dataset must use the type of gene identifiers. Use the function convertIDs, if a conversion is needed.

col

colour specification for the bars.

byType

logical that indicates if the colour specification in col should be interpreted as colours for each cell type. Is is used only when data is not missing. If TRUE then col specifies the colours to be used for all bars in each cell type. If FALSE

ylab

label for the y-axis. Default labels are provided if missing.

scale

logical that indicates if the data should be scaled. This argument is used only when beside=FALSE. If TRUE the gene expression profiles (rows of data) are scaled to sum up to 100, then the sample expression profiles (the columns of data) are scaled to sum up to 100. The scaled values can be interpreted as how much a marker gene is expressed in a sample relatively to other samples and genes.

legend

logical that indicates if a legend box should be added.

reorder

when data is missing, this argument indicates if/how the cell types should be reordered: FALSE do not reorder the cell types, a negative number orders by decreasing number of markers, and anything other than FALSE orders by increasing order of number of markers. When data is not missing, then it indicates if the markers should be ordered in the same order as they appear in the data. is used when data is not missing and indicates if the markers should be ordered as they appear in the dataset, as opposed to keep their original order, i.e. grouped by cell type.

las

specifies the orientation of the x-labels: 1 for horizontal, 2 for vertical.

...

extra arguments passed to barplot.

border

the color to be used for the border of the bars. Use border = NA to omit borders. If there are shading lines, border = TRUE means use the same colour for the border as for the shading lines.

beside

a logical value. If FALSE, the columns of height are portrayed as stacked bars, and if TRUE the columns are portrayed as juxtaposed bars.