Description Usage Arguments Value
Takes ExpressionSet object, performs PCA on the transposed expression matrix, then plots the projections of the sample scores on the specified PC.
1 2 3 |
cellData |
ExpressionSet object created with readCells (and preferably transformed with prepCells). It is also helpful to first run reduceGenes_var. |
center |
Boolean specifying whether to the center the data prior to PCA. This is generally recommended. |
scale |
Boolean specifying whether the data should be scaled prior to PCA. This is generally not recommended unless samples have different units (e.g. some samples are counts and some are TPMs). |
groups |
Character string specifying the title of the column in pData that contains the names of the groups to which each sample belongs. The dots representing each sample in the plot will be colored by group. The column length should be the same length as the number of samples. |
values |
Character string specifying the title of the column in pData that contains a vector of numeric values to be plotted as a color gradient on the dots in the plot. The column length should be the same length as the number of samples. Gene and values cannot be specified simultaneously. If groups and values are both specified, gene will be used for coloring. Set bubble to TRUE to display group information as well. |
gene |
Character string specifying a gene whose expression values will be plotted a color gradient on the dots in the plot. One gene name should be specified, and the gene must be present within the expression table. Gene and values cannot be specified simultaneously. If groups and gene are both specified, gene will be used for coloring. Set bubble to TRUE to display group information as well. |
colors |
Vector of character strings of length 2 specifying the color range for values or gene. If not specified, a default black-to-yellow color gradient will be used. |
logNumeric |
Boolean specifying whether the numbers in values should be transformed to log2 space. |
alpha |
Numeric specifying the transparency (from 0 to 1) level of the dot colors. |
dotsize |
Numeric specifying the size of the dots in the plot. |
bubble |
Boolean specifying whether dots of different sizes should be plotted to display information about another variable on the plot. |
bubbleSizes |
Vector of numerics specifying the dot sizes for each group within groups. Length of bubbleSizes should be the same length as groups. If bubbleSizes is not specified, default sizes will be generated according to the levels in the groups column. Useful for displaying group information along with values or gene. Additionally, can be used to indicate additional information about groups. E.g. if the levels in groups are 'A1', 'B1', 'C2', and 'D2', bubbleSizes could be c(3,3,6,6) to indicate the '1' and '2' components of the groups with different dot sizes. |
save |
Boolean specifying whether to save the resultant plot as a .tiff file. |
PCs |
Integer specifying the PC to plot. |
PCA plot for the specified PC.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.