I have generate a heatmap with pheatmap and for some reasons, I want that the rows appear in a predefined order.
I see in previous posts that the solution is to set the paramater cluster_row to FALSE, and to order the matrix in the order we want, like this in my case:
Otu0085 Otu0086 Otu0087 Otu0088 Otu0091
AB200 0 0 0 0 0
2 91 0 2 1 0
20CF360 0 1 0 1 0
19CF359 0 0 0 2 0
11VP12 0 0 0 0 155
11VP04 4 1 0 0 345
However, when I do:
pheatmap(shared,cluster_rows = F)
My rows are sorted alphabetically, like this:
10CF278a
11
11AA07
11CF278b
11VP03
11VP04
11VP05
11VP06
11VP08
11VP09
ANy suggestions would be welcome
Thank's by advance
Related
Hello everybody and thank you in advance for any help.
I inserted a txt file named "project" in R. This dataframe called "data" and consisted of 12 columns with some information of 999 households.
head(data)
im iw r am af a1c a2c a3c a4c a5c a6c a7c
1 0.00 20064.970 5984.282 0 38 0 0 0 0 0 0 0
2 15395.61 7397.191 0.000 42 30 1 0 0 0 0 0 0
3 16536.74 18380.770 0.000 33 28 1 0 0 0 0 0 0
4 20251.87 14042.250 0.000 38 38 1 1 0 0 0 0 0
5 17967.04 12693.240 0.000 24 39 1 0 0 0 0 0 0
6 12686.43 21170.450 0.000 62 42 0 0 0 0 0 0 0
im=male income
iw=female income
r=rent
am=male age
af=female age
a1c,a2c....a7c takes the value 1 when there is a child in age under 18
and the value 0 when there is not a child in the household.
Now i have to calculate the taxed income seperately for male and female for each houshold based on some criteria, so i am trying to create 1 function which calculate 2 numbers and after that to apply this function on my data frame and return a list with these numbers.
Specificaly I want something like this:
fact<-function(im,iw,r,am,af,a1c,a2c,a3c,a4c,a5c,a6c,a7c){
if ((am>0)&&(am<67)&&(af>0)) {mti<-im-(r)/2-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((am>0)&&(am<67)&&(af==0)) {mti<-im-r-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((am>=67)&&(af>0)) {mti<-im-1000-(r)/2-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((am<=67)&&(af==0)) {mti<-im-1000-r-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((af>0)&&(af<67)&&(am>0)) {fti<-iw-(r)/2-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((af>0)&&(af<67)&&(am==0)) {fti<-iw-r-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((af>=67)&&(am>0)) {fti<-iw-1000-(r)/2-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((af<=67)&&(am==0)) {fti<-iw-1000-r-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
return(mti,fti)}
how can i fix this function in order to apply on my dataframe?
Can a function return 2 values?
how can i apply the function?
THEN I TRIED THIS:
fact<-function(im=data$im,iw=data$iw,r=data$r,am=data$am,af=data$af,a1c=data$a1c,a2c=data$a2c,a3c=data$a3c,a4c=data$a4c,a5c=data$a5c,a6c=data$a6c,a7c=data$a7c){
if ((am>0)&&(am<67)&&(af>0)) {mti<-im-(r)/2-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((am>0)&&(am<67)&&(af==0)) {mti<-im-r-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((am>=67)&&(af>0)) {mti<-im-1000-(r)/2-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((am<=67)&&(af==0)) {mti<-im-1000-r-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((af>0)&&(af<67)&&(am>0)) {fti<-iw-(r)/2-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((af>0)&&(af<67)&&(am==0)) {fti<-iw-r-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((af>=67)&&(am>0)) {fti<-iw-1000-(r)/2-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
if ((af<=67)&&(am==0)) {fti<-iw-1000-r-(500*(a1c+a2c+a3c+a4c+a5c+a5c+a6c+a7c))}
return(mti,fti)}
fact(data[1,])
but i have tis error: Error in fact(data[1, ]) : object 'mti' not found
when i tried the function only for "fti" can run but wrongly.
Besides the need to return multiple values using c(mti, fti), your function doesn't have a default value if none of the conditions in the functions are TRUE. So, mti is never created.
Add mti <- NA at the start of your function, so NA is the default value.
I am currently working with about 301 rows of data and want to determine the earliest point at which only a few particular columns are nonzero. However, I also want to ensure that this does not change. For example, the two columns are nonzero, while all other columns are zero, then later in the dataframe other columns are nonzero as well, this would mean that I would have to determine a later point which is "correct".
I have the data:
1 x y z xx xy xz
292 0 -8.965140 9.596890 0 0 0 -0.03147483
293 0 -9.079889 9.645991 0 0 0 -0.02722520
294 0 -8.967767 9.597826 0 0 0 0
295 0 -9.090561 9.650230 0 0 0 -0.02685287
296 0 -9.081568 9.646105 0 0 0 -0.02716237
297 0 0.000000 0.000000 0 0 0 0.00000000
298 0 0.000000 0.000000 0 0 0 0.00000000
299 0 -9.098568 9.628576 0 0 0 -0.02654466
300 0 -9.089815 9.646099 0 0 0 -0.02681748
301 0 -8.998078 9.605140 0 0 0 0
As you can see, only the variables x and y are selected for row 294, however, the xz variable contains values after that until the 301 row. Is it possible to develop a function which tells me at which point is the minimum row where I see only x and y as nonzero and it remains that way until the final row of the dataframe?
I'm sorry if it's difficult to understand the question, I found it difficult asking how exactly to accomplish this issue.
EDIT: I presume I could use something like
which((df$x != 0 & df$y != 0 &
(df[, 1] | df[, 4] == 0))
but then I need to somehow expand the second or statement to all columns of df.
Thanks in advance.
I've been reading through a couple of the other useful guides on pulling player and match data from ESPN using R, however I have come across a problem with tabbed tables. As shown here on the player stats for a recent rugby game, the player statistics table is tabbed into 'Scoring', 'Attacking', 'Defending' and 'Discipline'.
Using the following code (with the help of two lovely packages (RCurl and htmltab), I can pull out the first tab ('Scoring') from that page ...
# install & attach RCurl
if (!base::require(package="RCurl")) utils::install.packages("RCurl")
library(RCurl)
# install & attach htmltab
if (!base::require(package="htmltab")) utils::install.packages("htmltab")
library(htmltab)
# assign URL
theurl <- RCurl::getURL("https://www.espn.co.uk/rugby/playerstats?gameId=294854&league=270557",.opts = list(ssl.verifypeer = FALSE))
# pull tables from url
team1 <- htmltab::htmltab(theurl,which=1)
team2 <- htmltab::htmltab(theurl,which=2)
league <- htmltab::htmltab(theurl,which=3)
... in the following format, which is exactly what I wanted ...
team1
rowID LEINS Tx TA CG PG PTS
2 J LarmourFB 0 0 0 0 0 0
3 H KeenanW 0 0 0 0 0 0
4 G RingroseC 0 0 0 0 0 0
5 R HenshawC 1 0 0 0 0 5
6 J LoweW 1 0 0 0 0 5
7 R ByrneFH 0 0 2 2 0 10
8 J Gibson-ParkSH 0 1 0 0 0 0
9 C HealyP 0 0 0 0 0 0
10 R KelleherH 0 0 0 0 0 0
11 A PorterP 0 0 0 0 0 0
... however I seem unable to pull out any tab other than 'Scoring'. I'm sure I'm missing something really obvious, so would appreciate someone pointing out where I'm going wrong!
Thanks in advance!
if you check the source html-page you will see that the data is not there at the start. You can find a data-reactid-tag that indicates that the data is only loaded once you click on the new tab. So you will need to find a way to make that click on the second tab.
One option for you might be to use Selenium: https://www.rdocumentation.org/packages/RSelenium/versions/1.7.7
This would enable you to make the necessary button click.
A sample can be found here: https://www.r-bloggers.com/2014/12/scraping-with-selenium/
I have a input uff file with 'n' no.of channels. I want to read the UFF file and also split the values based on each individual channel. Then store the result for each channel in separate file. Each channel always start with '-1' '58' etc., and end with '-1'.
Example channel_01 from the input UFF file:
-1
58
filename
22-Mar-2016 10:16:53
164
MnBrgFr-AC225R/N;50.9683995923 mV/m/s2
0 0 0 0 channel_01 0 0 NONE 0 0
2 1048576 1 0.00000E+00 8.19669930804e-06 0.00000E+00
17 0 0 0 Time s
1 0 0 0 MnBrgFr-AC225R/N m/s2
0 0 0 0 NONE NONE
0 0 0 0 NONE NONE
392.665124452 392.659048025 392.658404832 392.661676933 392.665882251 392.671989083
392.67634175 392.673743248 392.672398388 392.669360175 392.665533757 392.66088639
392.660390546 392.660975268 392.663400693 392.662668621 392.661209156 392.65498538
392.649463269 392.649580214 392.649259786 392.658580248 392.664715147 392.667051694
-1
I am currently trying to set up a heatmap of a matrix and highlight specific cells, based on two other matrices.
An example:
> SOI
NAP_G021 NAP_G033 NAP_G039 NAP_G120 NAP_G122
2315101 59.69418 27.26002 69.94698 35.22521 38.63995
2315102 104.15294 76.70379 114.72999 97.35930 79.46014
2315104 164.32822 61.83898 140.99388 63.25482 105.48041
2315105 32.15792 21.03730 26.89965 36.25943 40.46321
2315103 74.67434 82.49875 133.89709 93.17211 35.53019
> above150
NAP_G021 NAP_G033 NAP_G039 NAP_G120 NAP_G122
2315101 0 0 0 0 0
2315102 0 0 0 0 0
2315104 1 0 0 0 0
2315105 0 0 0 0 0
2315103 0 0 0 0 0
> below30
NAP_G021 NAP_G033 NAP_G039 NAP_G120 NAP_G122
2315101 0 1 0 0 0
2315102 0 0 0 0 0
2315104 0 0 0 0 0
2315105 0 1 1 0 0
2315103 0 0 0 0 0
Now I create a normal heatmap:
heatmap(t(SOI), Rowv = NA, Colv = NA)
Now what I want to do is highlight the cells, that have a 1 in above150 with a frame of one colour (e.g. blue), whilst the cells with a 1 in below30 should get a red frame. Of couse all matrices are equal sized as they are related. I know that I can add things to the heatmap after processing via add.expr, but so far I just managed to create full ablines that span the whole heatmap => not what I'm looking for.
If anybody has any suggestions I would be delighted.
When add.expr is called the plot is set so that the centre of the cells is at unit integer values. Try add.expr=points(1:5,1:5) to see. Now all you need to do is write a function that draws boxes (help(rect)) with the colours you need, at the half-integer coordinates.
Try this:
set.seed(310366)
nx=5
ny=6
SOI=matrix(rnorm(nx*ny,100,50),nx,ny)
colnames(SOI)=paste("NAP_G0",sort(as.integer(runif(ny,10,99))),sep="")
rownames(SOI)=sample(2315101:(2315101+nx-1))
above150 = SOI>150
below30=SOI<30
makeRects <- function(tfMat,border){
cAbove = expand.grid(1:nx,1:ny)[tfMat,]
xl=cAbove[,1]-0.49
yb=cAbove[,2]-0.49
xr=cAbove[,1]+0.49
yt=cAbove[,2]+0.49
rect(xl,yb,xr,yt,border=border,lwd=3)
}
heatmap(t(SOI),Rowv = NA, Colv=NA, add.expr = {
makeRects(above150,"red");makeRects(below30,"blue")})