| plotCtCategory {HTqPCR} | R Documentation |
This function will provide a summary of the featureCategory for a qPCRset. Focus can either be on categories across samples, or across features.
plotCtCategory(q, cards = TRUE, by.feature = FALSE, stratify, col, xlim, main, ...)
q |
object of class qPCRset. |
cards |
integers, the number of the cards (samples) to plot. |
by.feature |
logical, should the categories be summarised for features rather than samples. See details. |
stratify |
character string, either "type" or "class" indicating if the categories should be stratified by |
col |
vector with the colours to use for the categories. Default is green for "OK", yellow for "Unreliable" and red for "Undetermined". See details. |
xlim |
vector, the limits of the x-axis. If |
main |
character string, the title of the plot. |
... |
further arguments passed to |
This function is for generating two different types of plot. If by.feature=FALSE the number of each featureCategory will be counted for each card, and a barplot is made. If however by.feature=TRUE, then the categories for each feature across the selected cards will be clustered in a heatmap.
The colours given in col correspond to all the unique categories present in the entire featureCategory of q, even categories not represented for the samples selected by cards. Categories are sorted alphabetically, and colours assigned accordingly.
For by.feature=TRUE the plot can be modified extensively using calls to the underlying heatmap function, such as setting cexRow to adjust the size of row labels.
A figure is produced on the current graphics device.
Heidi Dvinge
setCategory, and heatmap for the underlying plotting function for by.feature=TRUE.
# Load example preprocessed data data(qPCRpros) # Plot categories for samples plotCtCategory(qPCRpros) plotCtCategory(qPCRpros, cards=1:3, stratify="class") # Categories for features plotCtCategory(qPCRpros, by.feature=TRUE)