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I am trying to create a forestplot, using forestplotter function, am able to get a beautiful graph, but am not able to see the entire graph, the column widths in few of the columns are so big, even if the string size is less, making the width of the entire graph, so big to see, can someone help me with this and also is it possible to align the datahrame contents uniformly centre aligned......Please help me with this
The code and relevant data are
###Required packages###
library(grid)
library(forestploter)
library(rmeta)
library(gridExtra)
#Data entered#
df <- data.frame(Study=c("A","B","C","D","Summary"),
nA = c(24,187,36,26,273),
median_A = c(4.9,5.69,8.866995074,8.5,NA),
Q1A =c(3,2.86,4.495073892,2,NA),
Q3A =c(8.5,9.78,14.96305419,32,NA),
nP = c(23,193,36,26,278),
median_P = c(7.2,6.79,8.990147783,12.5,NA),
Q1P =c(3.4,3.59,4.002463054,2,NA),
Q3P =c(10.9,10.12,12.06896552,43,NA),
W = c("10.6%","80.8%","8.0%","0.70%",NA),
E=c(-2.3,-1.1,-0.123152709,-4,-1.16881587),
UL=c(1.161473203,0.156288294,3.881699516,10.02689306,-0.039791047),
LL=c(-5.761473203,-2.356288294,-4.128004935,-18.02689306,-2.297840692))
#Calculate SE for box size#
df$SE <- (df$UL-df$E)/1.96
#Column for Confidence intervals for Drug A and Placebo, with 2 significant digit#
df$IQRA <- sprintf("%.2f (%.2f to %.2f)",df$median_A,df$Q1A, df$Q3A)
df$IQRP <- sprintf("%.2f (%.2f to %.2f)",df$median_P,df$Q1P, df$Q3P)
#Column for Confidence intervals for NET EFFECT, with 2 significant digit#
df$MD <- sprintf("%.2f (%.2f to %.2f)", df$E, df$LL, df$UL)
#Create a column with space for forest plot#
df$" "<- paste(rep(" ", 16), collapse = " ")
##Forest plot theme##
#To be modified as needed#
ftn <-forest_theme(
base_size = 16,
base_family = "serif",
ci_pch = 15,
ci_col = "black",
ci_lty = 1,
ci_lwd = 1,
ci_Theight = 0.25,
legend_name = " ",
legend_position = "right",legend_value = "",
xaxis_lwd = 1,
xaxis_cex = 0.7,
refline_lwd = 1,
refline_lty = "dashed",
refline_col = "red",
summary_fill = "blue",
summary_col = "blue",
footnote_cex = 0.4,
footnote_fontface = "plain",
footnote_col = "black",
title_just = c("center"),
title_cex = 1.1,
title_fontface = "bold",
title_col = "black",
show.rownames = FALSE)
##Table in Order for Forest plot##
#First get Column names#
colnames(df)
df2 <-df[,c(1,2,15,6,16,18,17)]
#Make NA cells empty
df2[5,3] <-c(" ")
df2[5,5] <-c(" ")
##Forestplot##
plot<-forest(df2,
est = df$E,
lower = df$LL,
upper = df$UL,
sizes = (df$SE/10),
ci_column = 6,
ref_line = 0,
arrow_lab = c("Drug A Better", "Placebo Better"),
xlim = c(-7, 6),
is_summary = c(FALSE,FALSE,FALSE,FALSE,TRUE),
xlog = FALSE,
ticks_digits = 0,ticks_at = c(-6,0,6),
theme = ftn)
##Show plot
print(plot, autofit = FALSE)
I have 5 variables which want to plot and export in one pdf. However, I have some trouble wiht the for-loop I am running,
parC <-list(unit = 100,labelx = "Time",labely = "Time",cols = "black",
pcex = .01, pch = 1,las = 1,
labax = seq(0,nrow(RP),100),
labay = seq(0,nrow(RP),100))
pdf("filename.pdf", onefile=TRUE)
for (i in RP_values){ # the values that are plotted
for (j in name) { # name is a list of names, so that the title changes dynamically
plotting(i, parC, j)
}
}
dev.off()
RP_values = list of values that is plotted
name = list of names to dynamically change the plotting title
plotting = an adjusted version from the plotRP() function of the crqa package. Here I added a main title to the plot.
The code for the plotting() function:
plotting <- function(RP, par, x){
if (exists("par") == FALSE){ # we use some defaults
## default values
unit = 2; labelx = "Time"; labely = "Time"
cols = "black"; pcex = .3; pch = 1; las = 0;
labax = seq(0, nrow(RP), unit); labay = seq(0, nrow(RP), unit);
} else { # we load the values that we desire
for (v in 1:length(par)) assign(names(par)[v], par[[v]])
}
xdim = nrow(RP)
ydim = ncol(RP)
RP = matrix(as.numeric(RP), nrow = xdim, ncol = ydim) # transform it for plotting
ind = which(RP == 1, arr.ind = T)
tstamp = seq(0, xdim, unit)
par(mar = c(5,5, 1, 3), font.axis = 2, cex.axis = 1,
font.lab = 2, cex.lab = 1.2)
plot(tstamp, tstamp, type = "n", xlab = "", ylab = "", xaxt = "n", yaxt = "n", main = x)
matpoints(ind[,1], ind[,2], cex = pcex, col = cols, pch = pch)
mtext(labelx, at = mean(tstamp), side = 1, line = 2.2, cex = 1.2, font = 2)
mtext(labely, at = mean(tstamp), side = 2, line = 2.2, cex = 1.2, font = 2)
# if (is.numeric(labax)){ ## it means there is some default
# mtext(labax, at = seq(1, nrow(RP), nrow(RP)/10), side = 1, line = .5, cex = 1, font = 2)
# mtext(labay, at = seq(1, nrow(RP), nrow(RP)/10), side = 2, line = .5, cex = 1, font = 2)
# } else{
mtext(labax, at = tstamp, side = 1, line = .5, cex = .8, font = 2, las = las)
mtext(labay, at = tstamp, side = 2, line = .5, cex = .8, font = 2, las = las)
# }
}
My problem is instead of 5 plots I get 25, where each plot appears 5 times, but with a different title. If I do not include the "j" part everything works fine, but of course do not have any main title for each plot.
I appreciate any help.
Best,
Johnson
From your description and comments, it appears you need an elementwise loop and not a nested loop. Consider retrieving all pairwise combinations of names and RP_values with expand.grid and iterate through them with mapply. Also, since parC depends on nrows of corresponding RP, have parC defined inside function for only two parameters (with more informative names like title instead of x):
plotting <- function(RP, title) {
parC <- list(unit=100, labelx="Time", labely="Time",
cols="black", pcex=.01, pch=1, las=1,
labax=seq(0, nrow(RP), 100),
labay=seq(0, nrow(RP), 100))
...
plot(tstamp, tstamp, type="n", xlab="", ylab="",
xaxt="n", yaxt="n", main=title)
...
}
params <- expand.grid(RP_values=RP_values, name=name)
out <- mapply(plotting, RP=params$RP_values, title=params$name)
I'm trying to create a phylogeny where the branch lengths that I've coded are represented by colour rather than length. So I want the branch lengths to be equal.
Here is my code:
plotBranchbyTrait(tree.scaled, tree.scaled$edge.length, mode=c("edges"),palette="rainbow", use.edge.length = FALSE, node.depth = 2)
It's my understanding that use.edge.length = FALSE should make the branch lengths equal, and it does this if I code the tree using plot.phylo(). But the tree still shows up with the branch lengths when I use plotBranchbyTrait(). Anyone know how to get around this?
Unfortunately, optional arguments (...) are not directly passed to plot.phylo in the plotBranchbyTrait function. One non-elegant way to fix that is to modify the body directly in R to add a hard coded use.edge.length = FALSE option.
You can do this by creating a new function and modify it using body(foo)[[line_of_interest]] <- substitute(my_new_line <- that_does_something). The following example should work:
## Back up the function
plotBranchbyTrait_no_edge_length <- phytools::plotBranchbyTrait
## The line to modify:
body(plotBranchbyTrait_no_edge_length)[[34]]
# xx <- plot.phylo(tree, type = type, show.tip.label = show.tip.label,
# show.node.label = show.node.label, edge.color = colors, edge.width = edge.width,
# edge.lty = edge.lty, font = font, cex = cex, adj = adj, srt = srt,
# no.margin = no.margin, root.edge = root.edge, label.offset = label.offset,
# underscore = underscore, x.lim = x.lim, y.lim = y.lim, direction = direction,
# lab4ut = lab4ut, tip.color = tip.color, plot = plot, rotate.tree = rotate.tree,
# open.angle = open.angle, lend = 2, new = FALSE)
## Modify the line 34 by adding `use.edge.length = FALSE`
body(plotBranchbyTrait_no_edge_length)[[34]] <- substitute( xx <- plot.phylo(use.edge.length = FALSE, tree, type = type, show.tip.label = show.tip.label, show.node.label = show.node.label, edge.color = colors, edge.width = edge.width, edge.lty = edge.lty, font = font, cex = cex, adj = adj, srt = srt, no.margin = no.margin, root.edge = root.edge, label.offset = label.offset, underscore = underscore, x.lim = x.lim, y.lim = y.lim, direction = direction, lab4ut = lab4ut, tip.color = tip.color, plot = plot, rotate.tree = rotate.tree, open.angle = open.angle, lend = 2, new = FALSE) )
## Testing whether it worked
library(phytools)
tree <- pbtree(n=50)
x <- fastBM(tree)
## With use.edge.length = TRUE (default)
plotBranchbyTrait(tree, x, mode = "tips", edge.width = 4, prompt = FALSE)
## With use.edge.length = FALSE
plotBranchbyTrait_no_edge_length(tree, x, mode = "tips", edge.width = 4, prompt = FALSE)
You can find more on how to modify functions here.
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(),
My goal is to assign a plot produced by the pyramid package to a list. Later, I will have that plot and others inserted from the list into a document. But the pyramid function appears not to return a value. How can I assign the pyramid plot to an object?
install.packages("pyramid") # functions to draw a population pyramid
library(pyramid)
# create a mock data frame to comparing this plot to a counterpart from plotrix
df <- data.frame(level1 = c(9,9,4,3,34,28), levelsame = c(9,9,4,3,34,28),
title = c("Dir", "Exec. Dir", "Mgr", "Sr. Mgr", "Mgt Princ", "EVP+"))
# assign the plot (hopefully) to an object
empty <- pyramid(df, Laxis = seq(1,35,5), AxisFM = "g", Csize = 0.8, Cgap = .5, Llab = "",
Rlab = "", Clab = "Title", GL = F, Lcol = "blue", Rcol = "blue",
Ldens = -1, main = "Distribution of Levels")
> empty
NULL
Likewise, if I assign the pyramid call to my list, nothing happens. There is no value for the list returned by pyramid.
plotlist2[["pyramid"]] <- pyramid(df, Laxis = seq(1,35,5), AxisFM = "g", Csize = 0.8, Cgap = .5, Llab = "",
Rlab = "", Clab = "Title", GL = F, Lcol = "blue", Rcol = "blue",
Ldens = -1, main = "Distribution of Levels")
> plotlist2[1]
[[1]]
NULL
I fear I am blundering in some obvious mis-understanding, so I welcome being set aright. Thank you.
You can use the recordPlot() function to save the current plot to a variable.
In your case you could do:
#print the plot
pyramid(df, Laxis = seq(1,35,5), AxisFM = "g", Csize = 0.8, Cgap = .5, Llab = "",
Rlab = "", Clab = "Title", GL = F, Lcol = "blue", Rcol = "blue",
Ldens = -1, main = "Distribution of Levels")
#save the current printed plot
pyrPlot<-recordPlot()
#plot it again
pyrPlot
You might have to enable the displaylist using dev.control(displaylist ="enable") for this to work depending on the graphical device you are using