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)