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Added support for heat maps of achieved growth on linear scale. Still having trouble with the input form in Rails.

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This commit is contained in:
Yury V Bukhman
2015-07-02 16:07:27 -05:00
parent 745f8a70af
commit 105be75c26
9 changed files with 82 additions and 39 deletions
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R/GCAT/man/create.heatmap.Rd
+3 -2
View File
@@ -4,7 +4,7 @@
\alias{create.heatmap}
\title{Create a heat map of a plate}
\usage{
create.heatmap(fitted.well.array, attribute, MinMax = NA, unlog = NULL)
create.heatmap(fitted.well.array, attribute, MinMax = NA, constant.added)
}
\arguments{
\item{fitted.well.array}{matrix containing well array object data}
@@ -13,7 +13,8 @@ create.heatmap(fitted.well.array, attribute, MinMax = NA, unlog = NULL)
\item{MinMax}{The specific range for the heatmap.}
\item{unlog}{transform values to linear scale}
\item{constant.added}{the numeric constant that was added to each curve before the log transform:
same as \code{add.constant} in \link{gcat.analysis.main}}
}
\value{
path of heatmap pdf file
R/GCAT/man/gcat.analysis.main.Rd
+10 -7
View File
@@ -8,12 +8,13 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
out.dir = getwd(), graphic.dir = paste(out.dir, "/pics", sep = ""),
add.constant = 0, blank.value, start.index, growth.cutoff = 0.05,
use.linear.param = F, use.loess = F, smooth.param = 0.1,
lagRange = NA, totalRange = NA, specRange = NA, points.to.remove = 0,
remove.jumps = F, time.input = NA, plate.nrow = 8, plate.ncol = 12,
input.skip.lines = 0, multi.column.headers = c("Plate.ID", "Well", "OD",
"Time"), single.column.headers = c("", "A1"),
layout.sheet.headers = c("Strain", "Media Definition"), silent = T,
verbose = F, return.fit = F, overview.jpgs = T)
lagRange = NA, totalRange = NA, totalODRange = NA, specRange = NA,
points.to.remove = 0, remove.jumps = F, time.input = NA,
plate.nrow = 8, plate.ncol = 12, input.skip.lines = 0,
multi.column.headers = c("Plate.ID", "Well", "OD", "Time"),
single.column.headers = c("", "A1"), layout.sheet.headers = c("Strain",
"Media Definition"), silent = T, verbose = F, return.fit = F,
overview.jpgs = T)
}
\arguments{
\item{file.list}{A list of full paths to .csv files. all files must be in the same format (see <single.plate>)}
@@ -42,7 +43,9 @@ gcat.analysis.main(file.list, single.plate, layout.file = NULL,
\item{lagRange}{The heatmap specific range for lag time.}
\item{totalRange}{The heatmap specific range for the achieved growth.}
\item{totalRange}{The heatmap specific range for the achieved growth on log scale.}
\item{totalODRange}{The heatmap specific range for the achieved growth on linear (OD) scale.}
\item{specRange}{The heatmap specific range for spec growth rate.}
R/GCAT/man/gcat.output.main.Rd
+4 -2
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@@ -9,8 +9,8 @@ gcat.output.main(fitted.well.array, out.prefix = "", source.file.list,
growth.cutoff, points.to.remove, remove.jumps, out.dir = getwd(),
graphic.dir = paste(out.dir, "/pics", sep = ""), overview.jpgs = T,
use.linear.param = F, use.loess = F, lagRange = NA, totalRange = NA,
specRange = NA, plate.nrow = 8, plate.ncol = 12, unlog = F,
silent = T, main.envir)
totalODRange = NA, specRange = NA, plate.nrow = 8, plate.ncol = 12,
unlog = F, silent = T, main.envir)
}
\arguments{
\item{fitted.well.array}{A list of fitted well objects.}
@@ -50,6 +50,8 @@ This is for backwards compatibility with the old web server.}
\item{totalRange}{The heatmap specific range for the achieved growth.}
\item{totalODRange}{The heatmap specific range for the achieved growth on linear (OD) scale.}
\item{specRange}{The heatmap specific range for spec growth rate.}
\item{plate.nrow}{The number of rows for a plate.}