Plot either old, new or total RNA of a gene in a row, per condition.
Usage
PlotGeneGroupsPoints(
data,
gene,
group = "Condition",
mode.slot = DefaultSlot(data),
columns = NULL,
log = TRUE,
show.CI = FALSE,
aest = NULL,
size = 2,
transform = NULL
)Arguments
- data
the grandR object to get the data to be plotted from
- gene
the gene to plot
- group
how to group the genes (default: Condition)
- mode.slot
the mode.slot of the grandR object to get the data from
- columns
which columns (i.e. samples or cells) to show (see details)
- log
show the y axis in log scale
- show.CI
show confidence intervals; one of TRUE/FALSE (default: FALSE)
- aest
parameter to set the visual attributes of the plot
- size
the point size used for plotting; overridden if size is defined via aest
- transform
function that is called on the data frame directly before plotting (can be NULL)
Details
The value of the aest parameter must be an Aesthetic mapping as generated by aes.
To refer to data slots, the mode.slot syntax can be used: Each name is either a data slot, or one of (new,old,total) followed by a dot followed by a slot. For new or old, the data slot value is multiplied by ntr or 1-ntr. This can be used e.g. to obtain the new counts.
The table used for plotting is the table returned by GetData with coldata set to TRUE, i.e. you can use all names from the Coldata table for aest.
By default, aest is set to aes(color=Condition,shape=Replicate) (if both Condition and Replicate are names in the Coldata table).
Columns can be given as a logical, integer or character vector representing a selection of the columns (samples or cells).
The expression is evaluated in an environment having the Coldata, i.e. you can use names of Coldata as variables to
conveniently build a logical vector (e.g., columns=Condition=="x").