R/bandle-plots.R
bandle-plots-translocations-table.RdProduces a table summarising differential localisation results
plotTable(params, all = FALSE, fcol)An instance of class bandleParams or an instance of
class MSnSetList of length 2.
A logical specifying whether to count all proteins or only show
those that have changed in location between conditions. Default is
FALSE.
If params is a list of MSnSets. Then
fcol must be defined. This is a character vector of length 2
to set different labels for each dataset. If only one label is specified,
and the character is of length 1 then this single label will be
used to identify the annotation column in both datasets.
Returns a summary table of translocations of proteins between conditions.
## Generate some example data
library("pRolocdata")
data("tan2009r1")
set.seed(1)
tansim <- sim_dynamic(object = tan2009r1,
numRep = 4L,
numDyn = 100L)
data <- tansim$lopitrep
control <- data[1:2]
treatment <- data[3:4]
## fit GP params
gpParams <- lapply(tansim$lopitrep, function(x)
fitGPmaternPC(x, hyppar = matrix(c(0.5, 1, 100), nrow = 1)))
## run bandle
res <- bandle(objectCond1 = control,
objectCond2 = treatment,
gpParams = gpParams,
fcol = "markers",
numIter = 5L,
burnin = 1L,
thin = 2L,
numChains = 2,
BPPARAM = SerialParam(RNGseed = 1),
seed = 1)
#>
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## Process bandle results
bandleres <- bandleProcess(res)
## Tabulate results
plotTable(bandleres)
#> Condition1 Condition2 value
#> 3 Cytoskeleton Lysosome 1
#> 6 Cytoskeleton Peroxisome 1
#> 7 Cytoskeleton Proteasome 3
#> 8 Cytoskeleton Ribosome 40S 1
#> 11 ER Cytoskeleton 3
#> 12 ER Golgi 16
#> 13 ER Lysosome 1
#> 16 ER Peroxisome 4
#> 17 ER Proteasome 2
#> 18 ER Ribosome 40S 1
#> 19 ER Ribosome 60S 2
#> 21 Golgi Cytoskeleton 5
#> 22 Golgi ER 2
#> 23 Golgi Lysosome 6
#> 24 Golgi Nucleus 1
#> 25 Golgi PM 12
#> 26 Golgi Peroxisome 2
#> 27 Golgi Proteasome 8
#> 28 Golgi Ribosome 40S 2
#> 29 Golgi Ribosome 60S 13
#> 30 Golgi mitochondrion 2
#> 43 Nucleus Golgi 2
#> 48 Nucleus Ribosome 40S 2
#> 49 Nucleus Ribosome 60S 1
#> 51 PM Cytoskeleton 3
#> 52 PM ER 2
#> 53 PM Golgi 7
#> 54 PM Lysosome 2
#> 55 PM Nucleus 1
#> 56 PM Peroxisome 3
#> 57 PM Proteasome 1
#> 58 PM Ribosome 40S 2
#> 59 PM Ribosome 60S 2
#> 61 Peroxisome Cytoskeleton 1
#> 71 Proteasome Cytoskeleton 4
#> 73 Proteasome Golgi 1
#> 77 Proteasome Peroxisome 1
#> 81 Ribosome 40S Cytoskeleton 3
#> 85 Ribosome 40S Nucleus 1
#> 87 Ribosome 40S Peroxisome 2
#> 88 Ribosome 40S Proteasome 1
#> 89 Ribosome 40S Ribosome 60S 5
#> 90 Ribosome 40S mitochondrion 3
#> 91 Ribosome 60S Cytoskeleton 1
#> 92 Ribosome 60S ER 1
#> 93 Ribosome 60S Golgi 1
#> 94 Ribosome 60S Lysosome 2
#> 97 Ribosome 60S Peroxisome 1
#> 99 Ribosome 60S Ribosome 40S 1
#> 101 mitochondrion Cytoskeleton 1
#> 104 mitochondrion Lysosome 2
#> 105 mitochondrion Nucleus 1
#> 106 mitochondrion PM 1
#> 107 mitochondrion Peroxisome 2
#> 109 mitochondrion Ribosome 40S 4
#> 110 mitochondrion Ribosome 60S 2