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fix R package dependencies #749

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Merged
teharrison merged 1 commit into from
Jul 2, 2015
Merged

fix R package dependencies #749

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7 changes: 5 additions & 2 deletions 7 dockerfiles/api/Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@ RUN apt-get update && apt-get install -y \
libpq-dev \
make \
curl \
r-base \
perl-modules \
liburi-perl \
libwww-perl \
Expand Down Expand Up @@ -36,12 +35,16 @@ RUN mkdir -p /var/log/httpd/api.metagenomics/ && \
cd /MG-RAST && \
make

# R dependencies
apt-get install -y r-base r-cran-nlme r-cran-ecodist && \
echo 'install.packages("matlab", repos = "http://cran.wustl.edu")' | R --no-save && \
echo 'source("http://bioconductor.org/biocLite.R"); biocLite("pcaMethods")' | R --no-save

# pipeline dependencies
RUN apt-get install -y \
python-dev \
python-pip \
libtemplate-perl

RUN pip install gspread xlrd openpyxl lepl
RUN cd / && git clone https://github.com/MG-RAST/pipeline.git

Expand Down
4 changes: 3 additions & 1 deletion 4 dockerfiles/web/Dockerfile
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Expand Up @@ -45,7 +45,9 @@ RUN cd / && git clone https://github.com/MG-RAST/pipeline.git

# 3rd party dependencies
RUN mkdir -p /tools && \
apt-get install -y gcc wget r-base
apt-get install -y gcc wget r-base r-cran-nlme r-cran-ecodist && \
echo 'install.packages("matlab", repos = "http://cran.wustl.edu")' | R --no-save && \
echo 'source("http://bioconductor.org/biocLite.R"); biocLite("pcaMethods")' | R --no-save
RUN cd /tools && \
wget circos.ca/distribution/circos-0.67-7.tgz && \
tar zxvf circos-0.67-7.tgz && \
Expand Down
40 changes: 20 additions & 20 deletions 40 src/MGRAST/r/dendrogram.r
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Expand Up @@ -97,10 +97,10 @@ MGRAST_dendrograms <<- function(
}

###### load the neccessary packages
if (produce_figures==TRUE)
{
suppressPackageStartupMessages(library(Cairo)) # (### indicates commented out to prevent production of the figure)
}
# if (produce_figures==TRUE)
# {
# suppressPackageStartupMessages(library(Cairo)) # (### indicates commented out to prevent production of the figure)
# }
##### by default, hclust(dist(object)) will produce a row dendrogram of the object
##### get the element counts for the imported object (this will be for the row dendrogram)
##### and for the 90 degree rotated version (for the column dendrogram)
Expand All @@ -124,14 +124,14 @@ MGRAST_dendrograms <<- function(
input_object_row_cluster <- hclust(find_dist(input_object, dist_method), method = clust_method)
input_object_clustered_row_order <- input_object_row_cluster$order

if (produce_figures==TRUE)
{
row_dendrogram_filename = paste(output_files_prefix, ".dist-", dist_method, "_clust-", clust_method, ".row_dendrogram.png")
row_dendrogram_filename = gsub(" ", "", row_dendrogram_filename)
CairoPNG(row_dendrogram_filename, width = row_dendrogram_width , height = row_dendrogram_height , units = "px")
plot(input_object_row_cluster, labels = input_object_row_cluster$labels, hang = -1, ann = FALSE, yaxs = "i") # THIS WORKS
dev.off()
}
# if (produce_figures==TRUE)
# {
# row_dendrogram_filename = paste(output_files_prefix, ".dist-", dist_method, "_clust-", clust_method, ".row_dendrogram.png")
# row_dendrogram_filename = gsub(" ", "", row_dendrogram_filename)
# CairoPNG(row_dendrogram_filename, width = row_dendrogram_width , height = row_dendrogram_height , units = "px")
# plot(input_object_row_cluster, labels = input_object_row_cluster$labels, hang = -1, ann = FALSE, yaxs = "i") # THIS WORKS
# dev.off()
# }
row_labels = matrix(0,1,(dim(matrix(input_object_row_cluster$labels))[1]))

for(i in 1:(dim(matrix(input_object_row_cluster$labels))[1]))
Expand All @@ -142,14 +142,14 @@ MGRAST_dendrograms <<- function(
input_object_col_cluster <- hclust(find_dist(input_object_rot_90, dist_method), method = clust_method)
input_object_clustered_col_order <- input_object_col_cluster$order

if (produce_figures==TRUE)
{
col_dendrogram_filename = paste(output_files_prefix, ".dist-", dist_method, "_clust-", clust_method, ".column_dendrogram.png")
col_dendrogram_filename = gsub(" ", "", col_dendrogram_filename)
CairoPNG(col_dendrogram_filename, width = col_dendrogram_width , height = col_dendrogram_height , units = "px")
plot(input_object_col_cluster, labels = input_object_col_cluster$labels, hang = -1, ann = FALSE, yaxs = "i")
dev.off()
}
# if (produce_figures==TRUE)
# {
# col_dendrogram_filename = paste(output_files_prefix, ".dist-", dist_method, "_clust-", clust_method, ".column_dendrogram.png")
# col_dendrogram_filename = gsub(" ", "", col_dendrogram_filename)
# CairoPNG(col_dendrogram_filename, width = col_dendrogram_width , height = col_dendrogram_height , units = "px")
# plot(input_object_col_cluster, labels = input_object_col_cluster$labels, hang = -1, ann = FALSE, yaxs = "i")
# dev.off()
# }
col_labels = matrix(0,1,(dim(matrix(input_object_col_cluster$labels))[1]))

for(i in 1:(dim(matrix(input_object_col_cluster$labels))[1]))
Expand Down
50 changes: 25 additions & 25 deletions 50 src/MGRAST/r/plot_pca.r
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Expand Up @@ -33,31 +33,31 @@ MGRAST_plot_pca <<- function(file_in,

my_pcaRes <<- pca(input_object, nPcs = num_PCs) # Run pca and create pcaRes object

if (produce_fig == TRUE){ # option to produce figure

suppressPackageStartupMessages(library(Cairo))

CairoPNG(image_out, width = figure_width, height = figure_height, pointsize = 12, res = figure_res , units = "px")

plot(my_pcaRes@loadings[,PC1],
my_pcaRes@loadings[,PC2],
cex.axis = axis_cex,
cex.lab = lab_cex,
main = image_title,
type = "p",
col = points_color,
xlab = paste(PC1, "R^2 =", round(my_pcaRes@R2[PC1], 4)),
ylab = paste(PC2, "R^2 =", round(my_pcaRes@R2[PC2], 4))
)

if (points_color != 0){
points(my_pcaRes@loadings[,PC1], my_pcaRes@loadings[,PC2], col = points_color, pch=19, cex=2 )
# color in the points if the points_color option has a value other than NA
# pch, integer values that indicate different point types (19 is a filled circle)
}

text(my_pcaRes@loadings[,PC1], my_pcaRes@loadings[,PC2], labels=rownames(my_pcaRes@loadings), cex = points_text_cex)
}
# if (produce_fig == TRUE){ # option to produce figure
#
# suppressPackageStartupMessages(library(Cairo))
#
# CairoPNG(image_out, width = figure_width, height = figure_height, pointsize = 12, res = figure_res , units = "px")
#
# plot(my_pcaRes@loadings[,PC1],
# my_pcaRes@loadings[,PC2],
# cex.axis = axis_cex,
# cex.lab = lab_cex,
# main = image_title,
# type = "p",
# col = points_color,
# xlab = paste(PC1, "R^2 =", round(my_pcaRes@R2[PC1], 4)),
# ylab = paste(PC2, "R^2 =", round(my_pcaRes@R2[PC2], 4))
# )
#
# if (points_color != 0){
# points(my_pcaRes@loadings[,PC1], my_pcaRes@loadings[,PC2], col = points_color, pch=19, cex=2 )
# # color in the points if the points_color option has a value other than NA
# # pch, integer values that indicate different point types (19 is a filled circle)
# }
#
# text(my_pcaRes@loadings[,PC1], my_pcaRes@loadings[,PC2], labels=rownames(my_pcaRes@loadings), cex = points_text_cex)
# }

write.table(my_pcaRes@R2, file=file_out, sep="\t", col.names=FALSE, row.names=TRUE, append = FALSE)
write.table(loadings(my_pcaRes), file=file_out, sep="\t", col.names=FALSE, row.names=TRUE, append = TRUE)
Expand Down
20 changes: 10 additions & 10 deletions 20 src/MGRAST/r/preprocessing.r
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Expand Up @@ -131,15 +131,15 @@ MGRAST_preprocessing <<- function(file_in, # name of the input file (tab del
###### write the log transformed and centered data to a file
write.table(log2_cent_data, file=file_out, sep="\t", col.names = NA, row.names = TRUE, quote = FALSE)

if (produce_fig == TRUE){ # optional - produce an out put image
suppressPackageStartupMessages(library(Cairo))
CairoPNG(image_out, width = figure_width, height = figure_height, pointsize = 12, res = fiure_res , units = "px")
split.screen(c(2,1))
screen(1)
boxplot(input_data, main = raw_data_boxplot_title, las=2)
screen(2)
boxplot(log2_cent_data, main = centered_data_boxplot_title, las=2)
dev.off()
}
# if (produce_fig == TRUE){ # optional - produce an out put image
# suppressPackageStartupMessages(library(Cairo))
# CairoPNG(image_out, width = figure_width, height = figure_height, pointsize = 12, res = fiure_res , units = "px")
# split.screen(c(2,1))
# screen(1)
# boxplot(input_data, main = raw_data_boxplot_title, las=2)
# screen(2)
# boxplot(log2_cent_data, main = centered_data_boxplot_title, las=2)
# dev.off()
# }

}
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