ExperimentColorMap-class {iSEE} | R Documentation |
ExperimentColorMap class
ExperimentColorMap(assays = list(), colData = list(), rowData = list(), all_discrete = list(assays = NULL, colData = NULL, rowData = NULL), all_continuous = list(assays = NULL, colData = NULL, rowData = NULL), global_discrete = NULL, global_continuous = NULL, ...)
assays |
List of color maps for |
colData |
List of color maps for |
rowData |
List of color maps for |
all_discrete |
Discrete color maps applied to all undefined
|
all_continuous |
Continuous color maps applied to all undefined
|
global_discrete |
Discrete color maps applied to all undefined discrete covariates. |
global_continuous |
Continuous color maps applied to all undefined discrete covariates. |
... |
additional arguments passed on to the |
Color maps must all be functions that take at least one argument: the number
of (named) colours to return as a character
vector.
This argument may be ignored in the body of the color map function
to produce constant color maps.
An object of class ExperimentColorMap
In the following code snippets, x
is an
ExperimentColorMap
object. If the color map can not immediately
be found in the appropriate slot, discrete
is a logical(1)
that indicates whether the default color map returned should be discrete
TRUE
or continuous (FALSE
, default).
assayColorMap(x, i, ..., discrete=FALSE)
:Get an assays
colormap.
colDataColorMap(x, i, ..., discrete=FALSE)
:Get a colData
colormap.
rowDataColorMap(x, i, ..., discrete=FALSE)
:Get a rowData
colormap.
In the following code snippets, x
is an
ExperimentColorMap
object, and .
assayColorMap(x, i, ...) <- value
:Set an assays
colormap.
colDataColorMap(x, i, ...) <- value
:Set a colData
colormap.
rowDataColorMap(x, i, ...) <- value
:Set a rowData
colormap.
assay(x, i, ...) <- value
:Alias. Set an assays
colormap.
# Example color maps ---- count_colors <- function(n){ c("black","brown","red","orange","yellow") } fpkm_colors <- viridis::inferno tpm_colors <- viridis::plasma qc_color_fun <- function(n){ qc_colors <- c("forestgreen", "firebrick1") names(qc_colors) <- c("Y", "N") return(qc_colors) } # Constructor ---- ecm <- ExperimentColorMap( assays = list( counts = count_colors, tophat_counts = count_colors, cufflinks_fpkm = fpkm_colors, rsem_tpm = tpm_colors ), colData = list( passes_qc_checks_s = qc_color_fun ) ) # Accessors ---- # assay color maps assayColorMap(ecm, "logcounts") # [undefined --> default] assayColorMap(ecm, "counts") assayColorMap(ecm, "cufflinks_fpkm") assay(ecm, "cufflinks_fpkm") # alias # colData color maps colDataColorMap(ecm, "passes_qc_checks_s") colDataColorMap(ecm, "undefined") # rowData color maps rowDataColorMap(ecm, "undefined") # generic accessors assays(ecm) assayNames(ecm) # Setters ---- assayColorMap(ecm, "counts") <- function(n){c("blue","white","red")} assay(ecm, 1) <- function(n){c("blue","white","red")} colDataColorMap(ecm, "passes_qc_checks_s") <- function(n){NULL} rowDataColorMap(ecm, "undefined") <- function(n){NULL}