I am using a particular R package called wTO (https://cran.r-project.org/web/packages/wTO/index.html)
One of the function which does the main computation also creates a plot among other things. As I am running the scripts on a CentOS server using SSH, I would like to save the plots. I am not sure where I should insert the commands for saving the plots. Kindly help.
The command is
> x= wTO.Complete(k = 32, n = 100, Data, Overlap, method = "p", method_resampling = "Bootstrap", pvalmethod = "BH", savecor = F, expected.diff = 0.2, lag = NULL, normalize = F, plot = T)
You need to open a graphic device before you call the function:
http://stat.ethz.ch/R-manual/R-devel/library/grDevices/html/png.html
After opening every plot will be written to this device until you call dev.off().
So you would do:
jpeg(filename = "yourname.jpeg")
x= wTO.Complete(k = 32, n = 100, Data, Overlap, method = "p", method_resampling = "Bootstrap", pvalmethod = "BH", savecor = F, expected.diff = 0.2, lag = NULL, normalize = F, plot = T)
dev.off()
You can then use/transfer your plot saved in yourname.jpeg.
Related
For 3D visualizaiton used matrix data. Package: Rayshader 0.34.0.
The data is can be seen in render_camera but using high_quality function facing problem in saving rendeeing out put.
Error in rayrender::obj_model(cache_filename, x = -bbox_center[1], y = -bbox_center[2], :
unused argument (texture = TRUE)
I was expecting a render image so that my 3d map can be saved in png format with rendering quality.
mat |>
height_shade(texture = textr) |>
plot_3d(heightmap = mat,
zscale = 1000,
solid = FALSE,
shadowdepth = 0)
render_camera(theta = -100, phi = 30, zoom = .7)
render_highquality("E:/URP/R/3D Bangladesh/DATA/Images/tp.png",
samples = 450,
preview = FALSE,
light = TRUE,
lightdirection = c(135, 45),
lightcolor = c("white"),
lightintensity = c(800),
ambient_light = 0.5,
shadow_intensity = 0.5,
zscale = 1,
width = 8000, height = 8000,
interactive = FALSE)
Install most recent dev versions of rayshader and rayrender.
remotes::install_github("https://github.com/tylermorganwall/rayshader")
remotes::install_github("https://github.com/tylermorganwall/rayrender")
Same issue.
I've tried to install the most recent dev versions but probably I do something wrong.
What do I have to choose here (and later similarly for rayrender)?
terminal options
If I choose "All" at every steps I get some conflicts
I tried to plot star plots with individual label in R but could not achieve it.
This is a picture of what I want my starplots to look like:
This is what I got after running the code below:
# loading package
library(fmsb)
# loading data
dac<- read_excel("Mean_data_ESS.xlsx")#reading from the .xlsx fil
daks<-select(dac, Pollinators,Flower_abundance,
Climate_regulation,Crop_area,
Plant_diversity,Nitrogen_balance,
Phosphorus_balance,Habitat_provision,
Recreation_covid,Aesthetic_appreciation,
Reconnection_nature,Mental_health,
Physical_health)
process <- preProcess(as.data.frame(daks), method=c("range"))
norm_datas <- predict(process, as.data.frame(daks))
stars(norm_datas[, 1:12], full = TRUE,radius = TRUE,len = 1.0,
key.loc = c(14,1),
labels = abbreviate(case.names(norm_datas)),
main = "Provision of Ecosystem services", draw.segments = TRUE,
lwd = 0.25, lty = par("lty"), xpd = TRUE)
I am using WGCNA package for network analysis with following steps:
Data input
Generate Modules
Get gene id
Phenotype x module correlation
I want to use the package to include the phenotype data together with the gene expression matrix to find which genes group with the phenotypes. Then, I want to get the module of interest and do a network map and check which genes relate to the phenotypes.
I generated modules like:
library(WGCNA)
options(stringsAsFactors = FALSE)
enableWGCNAThreads()
lnames = load(file = "dataInput.RData");
# Choose a set of soft-thresholding powers
powers = c(c(1:10), seq(from = 12, to=40, by=2))
# Call the network topology analysis function
sft = pickSoftThreshold(datExpr, powerVector = powers, verbose = 5)
# Plot the results:
sizeGrWindow(9, 5)
par(mfrow = c(1,2));
cex1 = 0.9;
# Scale-free topology fit index as a function of the soft-thresholding power
plot(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],
xlab="Soft Threshold (power)",ylab="Scale Free Topology Model Fit,signed R^2",type="n",
main = paste("Scale independence"));
text(sft$fitIndices[,1], -sign(sft$fitIndices[,3])*sft$fitIndices[,2],
labels=powers,cex=cex1,col="red");
# this line corresponds to using an R^2 cut-off of h
abline(h=0.90,col="red")
# Mean connectivity as a function of the soft-thresholding power
plot(sft$fitIndices[,1], sft$fitIndices[,5],
xlab="Soft Threshold (power)",ylab="Mean Connectivity", type="n",
main = paste("Mean connectivity"))
text(sft$fitIndices[,1], sft$fitIndices[,5], labels=powers, cex=cex1,col="red")
##Constructing the gene network and identifying modules is now a simple function call:
net_unsigned = blockwiseModules(datExpr, power = 6,
TOMType = "unsigned", minModuleSize = 30, maxBlockSize = 300,
reassignThreshold = 0, mergeCutHeight = 0.25,
numericLabels = TRUE, pamRespectsDendro = FALSE,
saveTOMs = TRUE,
saveTOMFileBase = "PopulusTOM_signed",
verbose = 5)
##maxBlockSize = The total number of genes you have in your gene expression matrix that passed the filter from Data_Input scrip
##Plotting graph
pdf("Dendogram_Modules_signed.pdf", width = 30, height = 30);
##Convert labels to colors for plotting
mergedColors = labels2colors(net_unsigned$colors)
##Plot the dendrogram and the module colors underneath
plotDendroAndColors(net_unsigned$dendrograms[[1]], mergedColors[net_unsigned$blockGenes[[1]]],
"Module colors",
dendroLabels = FALSE, hang = 0.03,
addGuide = TRUE, guideHang = 0.05)
dev.off()
##Save
moduleLabels = net_unsigned$colors
moduleColors = labels2colors(net_unsigned$colors)
MEs = net_unsigned$MEs;
geneTree = net_unsigned$dendrograms[[1]];
save(MEs, moduleLabels, moduleColors, geneTree,
file = "unsigned-networkConstruction-auto.RData")
This generates modules and then I correlated a module with one phenotype. How can I include the phenotypic data with gene expression? Thank you!
I have SSIS package that gets data into database and then executes R Script. R script creates new folder (names it based on the current date) and generate some pdf files into this folder. I have deployed this package on server and created Job that executes it every night. The problem is that each morning I am finding only empty folders (with correct date name) without any pdf files. However, If I execute that package manually in Visual Studio it works fine and pdfs are there. Am I missing something here? I appreciate every answer.
EDIT
When I execute manually it is directly on the server
Package looks like this
and here is my R script
dir.create(file.path(output.path, date))
library(RODBC)
conn <- odbcConnect("Azure", uid = "aaaaa", pwd = "aaaaa")
etldata <- sqlFetch(conn,"dbo.EtlLogsData", stringsAsFactors = FALSE)
pdf(paste('ETL_Duration_For_Effective_Date_', date,'.pdf',sep = ""),
width = 12,
height = 8,
paper = 'special')
par(mar = c(5, 17, 5, 3))
plot(c(min(etldata_day$st_sec), max(etldata_day$et_sec)),
c(sn[1], sn[1]),
ylim = c(0, n),
yaxt = 'n',
xaxt = 'n',
ylab = '',
xlab = 'Time',
main = paste('ETL Duration With Effective Date ', date, sep = ""))
abline(h = sn, untf = FALSE, col = "gray90")
for (i in 1:n){
lines(c(etldata_day$st_sec[i], etldata_day$et_sec[i]),
c(sn[i], sn[i]),
type = "l", lwd = 2)
arrows(etldata_day$st_sec[i], sn[i],
etldata_day$et_sec[i], sn[i],
length = 0.025, angle = 90, lwd = 2)
arrows(etldata_day$et_sec[i], sn[i],
etldata_day$st_sec[i], sn[i],
length = 0.025, angle = 90, lwd = 2)
}
# Print y axis labels
axis(2, at = sn, labels = etldata_day$TaskName, las = 1, cex.axis = 1)
# Print x axis labels
xat <- seq(from = min(etldata_day$st_sec), to = max(etldata_day$et_sec), length.out = 10)
xlabels <- secondsToString(xat)
axis(1, at = xat, labels = substr(xlabels,1,8), cex.axis = 1)
dev.off()
After plot() I use some FOR cycles, and LINES(),
I am plotting a time series with the timePlot function of the open air package of R. The graph has grey grid lines in the background that I would like to turn off but I do not find a way to do it. I would expect something simple such as grid = FALSE, but that is not the case. It appears to be rather complex, requiring the use of extra arguments which are passed to xyplot of the library lattice. I believe the answer lies some where in the par.settings function but all attempts have failed. Does anyone have any suggestions to this issue?
Here is by script:
timeozone <- import(i, date="date", date.format = "%m/%d/%Y", header=TRUE, na.strings="")
ROMO = timePlot(timeozone, pollutant = c("C7", "C9", "C10"), group = TRUE, stack = FALSE,y.relation = "same", date.breaks = 9, lty = c(1,2,3), lwd = c(2, 3, 3), fontsize = 15, cols = c("black", "black"), ylab = "Ozone (ppbv)")
panel = function(x, y) {
panel.grid(h = 0, v = 0)
panel.xyplot(x,y)
}