iSEE (version 0.98.2)

ExperimentColorMap: ExperimentColorMap objects

Description

ExperimentColorMap objects

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

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.

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.

Examples

# NOT RUN {
# 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,
        cufflinks_fpkm = fpkm_colors,
        rsem_tpm = tpm_colors
    ),
    colData = list(
        passes_qc_checks_s = qc_color_fun
    )
)

# Accessors ----

assayColorMap(ecm, "logcounts") # [undefined --> default]
assayColorMap(ecm, "counts")
assayColorMap(ecm, "cufflinks_fpkm")

colDataColorMap(ecm, "passes_qc_checks_s")
colDataColorMap(ecm, "undefined")

rowDataColorMap(ecm, "undefined")

# }