ExperimentColorMap-class {iSEE}R Documentation

ExperimentColorMap class

Description

ExperimentColorMap class

Usage

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, ...)

Arguments

assays

List of color maps for assays.

colData

List of color maps for colData.

rowData

List of color maps for rowData.

all_discrete

Discrete color maps applied to all undefined assays, colData, and rowData, respectively.

all_continuous

Continuous color maps applied to all undefined assays, colData, and rowData, respectively.

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 ExperimentColorMap constructor

Details

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.

Value

An object of class ExperimentColorMap

Accessors

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.

Setters

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.

Examples


# 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}
[Package iSEE version 1.0.1 Index]