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Remove left-over code
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Remove left-over code from user specified sample shift/strech support.
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@mschilli87
mschilli87 committed May 17, 2018
1 parent 5273eae commit 4012c3f
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Showing 2 changed files with 14 additions and 263 deletions.
238 changes: 5 additions & 233 deletions functions.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,8 @@
# change log (reverse chronological) #
######################################

# 2018-04-13: removed support for user specified sample shifts
# 2018-04-13: removed left-over code from user specified sample shift/strech support
# removed support for user specified sample shifts
# added support for default ymin/max values
# parameterized span to use for smoothing for 3D model
# added 3D model CPM fitting and coloring support
Expand Down Expand Up @@ -287,74 +288,6 @@ generate.manual.ymax.input<-
# end y-axis maximum input panel generation function definition
}

# get sample stretch input names by sample name
get.sample.stretch.inputId<-

# define sample stretch input name function
function(

# sample name to get sample stretch input name for
sample.name

# end sample stretch input name function parameter definition
)

# begin sample stretch input name function definition
{

# take sample name to get sample stretch input name for
sample.name %>%

# add sample stretch input name prefix
paste0("sample.stretch.",.)

# end sample stretch input name function definition
}

# generate sample stretch input panel
generate.sample.stretch.input<-

# define sample stretch input panel generation function
function(

# sample name of generate sample stretch input panel for
sample.name

# end sample stretch input panel generation function parameter definition
)

# begin sample stretch input panel generation function definition
{

# take sample name of generate sample stretch input panel for
sample.name %>%

# generate sample stretch input panel
sliderInput(

# name sample stretch input value
inputId=get.sample.stretch.inputId(.)

# label sample stretch input panel
,label=.

# set sample stretch input panel minimum value
,min=params$sample.stretches.input.min

# set sample stretch input panel maximum value
,max = params$sample.stretches.input.max,

value = input.data$sample.stretch.defaults[sample.name],

# set sample stretch input panel value suffix
post = params$sample.stretches.input.suffix

# end sample stretch input panel generation
)

# end sample stretch input panel generation function definition
}

# parse gene names input from single string to vector
parse.gene.names<-

Expand Down Expand Up @@ -485,51 +418,6 @@ filter.data.by.expression.level<-
}


# convert named sample stretch list (or NULL) to named (default) sample stretch vector
parse.sample.stretches<-

# define sample stretch conversion function
function(

# list with sample stretches labeled with sample names (or NULL)
stretches

# sample names to include in output sample stretch vector
,samples

# end sample stretch conversion function parameter definition
)

# begin sample stretch conversion function definition
{

# if no sample stretches were specified, use default values
if(is.null(stretches))

# take default sample stretch input value
params$sample.stretches.input.default %>%

# repeat for each sample specified
rep(times=length(samples)) %>%

# label default sample stretches with sample names
setNames(samples)

# if sample stretches were specified, convert list to vector
else

# take sample names to include in output sample stretch vector
samples %>%

# extract corresponding sample stretches
stretches[.] %>%

# convert names list to vector
unlist

# end sample stretch conversion function definition
}

# add shift column to data
add.shift.column<-

Expand Down Expand Up @@ -1768,40 +1656,6 @@ get.gene.table.xlsx.name<-
# data extraction functions #
#############################

# extract sample stretch inputs from inputs list
get.sample.stretches<-

# define sample stretch input extraction function
function(

# sample names of samples to extract sample stretch inputs for
sample.names

# input list to extract sample stretch inputs from
,inputs

# end sample stretch input extraction function parameter definition
)

# begin sample stretch input extraction function definition
{

# take sample names of samples to extract sample stretch inputs for
sample.names %>%

# get corresponding sample stretch input names
get.sample.stretch.inputId %>%

# extract sample stretch inputs from input list by input names
llply(. %>% inputs[[.]]) %>%

# label sample stretch inputs with sample names
setNames(sample.names)

# end sample stretch input extraction function definition
}


# extract gene annotation from gene profiles table
get.gene.annotation<-

Expand Down Expand Up @@ -2097,68 +1951,6 @@ fit.cpm <-
# input panel functions #
#########################

# sample shifts input panel generation
generate.sample.shifts.input<-

# define sample shifts input panel generation function
function(

# sample names to include in sample shifts input panel
sample.names

# end sample shifts input panel generation function parameter definition
)

# begin sample shifts input panel generation function
{

# take sample names to include in sample shifts input panel
sample.names %>%

# generate sample shift input panel per sample
llply(

# generate sample shift input panel
generate.sample.shift.input

# end sample shift input panel generate per sample
)

# end sample shifts input panel generation function
}


# sample stretches input panel generation
generate.sample.stretches.input<-

# define sample stretches input panel generation function
function(

# sample names to include in sample stretches input panel
sample.names

# end sample stretches input panel generation function parameter definition
)

# begin sample stretches input panel generation function
{

# take sample names to include in sample stretches input panel
sample.names %>%

# generate sample stretch input panel per sample
llply(

# generate sample stretch input panel
generate.sample.stretch.input

# end sample stretch input panel generate per sample
)

# end sample stretches input panel generation function
}


# generate genotype input panel
generate.genotype.input<-

Expand Down Expand Up @@ -2304,12 +2096,10 @@ generate.profile.plot<-

# sample stretch input list
sample.stretches =

# use default sample stretch input values for all samples by default
NULL
input.data$sample.stretch.defaults,

# plot isoform-specific profiles?
,per.isoform=
per.isoform =

# by default, plot gene level profiles
FALSE,
Expand Down Expand Up @@ -2376,25 +2166,7 @@ generate.profile.plot<-
add.shift.column(shifts.by.sample = sample.shifts) %>%

# add stretch column to data
add.stretch.column(

# specify stretches to add by sample
stretches.by.sample=

# take sample stretch
sample.stretches %>%

# convert named list (or NULL) to named vector
parse.sample.stretches(

# specify samples to convert sample stretches for
samples=sample.names

# end sample stretch conversion
)

# end addition of stretch column
) %>%
add.stretch.column(stretches.by.sample = sample.stretches) %>%

# plot profiles based on filtered tomo-seq data
plot.profiles(
Expand Down
39 changes: 9 additions & 30 deletions params.R
View file
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,8 @@
# change log (reverse chronological) #
######################################

# 2018-04-13: added default ymin/max values
# 2018-04-13: removed un-needed parameters left over from sample shift/stretch input panels
# added default ymin/max values
# adjusted sample description and genotype defaults
# added 3D model colorbar parameters
# added 3D model tab & plot parameters
Expand Down Expand Up @@ -296,40 +297,18 @@ if(!exists("params"))
# sample shifts input panel #
#############################

# label of sample shift input panel
sample.shifts.input.label = "Sample shifts"

# minimum value of sample shift input panel
,sample.shifts.input.min=-50

# maximum value of sample shift input panel
,sample.shifts.input.max=50

# default value of sample shift input panel
,sample.shifts.input.default=0

# value suffix of sampleshift input panel
,sample.shifts.input.suffix="%"
sample.shifts.input.min = -50,
sample.shifts.input.max = 50,
sample.shifts.input.default = 0,


################################
# sample stretches input panel #
################################

# label of sample shift input panel
,sample.stretches.input.label="Sample stretches"

# minimum value of sample shift input panel
,sample.stretches.input.min=.5

# maximum value of sample shift input panel
,sample.stretches.input.max=2

# default value of sample shift input panel
,sample.stretches.input.default=1

# value suffix of sampleshift input panel
,sample.stretches.input.suffix="x"
sample.stretches.input.min = .5,
sample.stretches.input.max = 2,
sample.stretches.input.default = 1,


##############
Expand All @@ -349,7 +328,7 @@ if(!exists("params"))
#####################

# title of heatmap tab panel
,heatmap.tab.title="Heatmap"
heatmap.tab.title = "Heatmap"


#################
Expand Down

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