haotu : an open lab notebook

2018/01/03

All Pairwise Combinations of Rownames from a Square Matrix

Filed under: R, R, R spatial, R Stats, Uncategorized — Tags: , , , — S @ 12:37
combn(rownames(my.square.matrix), m=2, FUN=paste, collapse = "-", simplify = T)
Advertisements

2017/07/18

Make ggplot look like base plot in R

Filed under: ggplot, R, R graphics — Tags: , , , , , , — S @ 04:46
myplot + theme_bw() + theme(panel.border = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))
myplot + theme_bw() + theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank(), axis.line = element_line(colour = "black"))

here

 

 

 

2017/06/22

Automatic MIT License for R Packages

Filed under: errors in R, R, R Stats — Tags: , — S @ 07:01
devtools::use_mit_license()

2016/06/24

save rda data file with compression

Filed under: errors in R, R, R, R Stats — Tags: , , , , — S @ 06:36
save(mydata,file="mydata.rda",compress="xz")

find non-ascii in R

Filed under: errors in R, R, R, R Stats, Uncategorized — Tags: , , , , — S @ 06:34
tools::showNonASCII(readLines("myfiles.R"))

2016/04/18

raster cell area size 1 degree cell size km2

Filed under: R, R spatial, R Stats, Uncategorized — Tags: , — S @ 08:14

For a 1×1 degree cell size raster

r <- raster(ncol=360, nrow=180) #or just the default r<-raster()
area(r)
area(r)$values

 

http://gis.stackexchange.com/questions/177622/r-calculate-raster-cell-size-in-map-units

 

http://gis.stackexchange.com/questions/29734/how-to-calculate-area-of-1-x-1-degree-cells-in-a-raster

2015/02/02

new faster code for PGLMM

Filed under: Uncategorized — Tags: , , — S @ 11:50

https://github.com/willpearse/pez/blob/master/R/pglmm.R

2015/01/30

aggregate more than one column in data.table

Filed under: R — Tags: , , , , — S @ 11:15
# Average ability by grade
agg1<- fm1[, j=list(mean(x0, na.rm = TRUE),mean(x1, na.rm = TRUE)),by = key]

http://rprogramming.net/aggregate-data-in-r-using-data-table/

2014/11/07

BLAST from R

Filed under: Uncategorized — Tags: , , , , , , — S @ 08:16

There is a nice post here on the topic
The post takes code from the blastSequences function in the R package annotate

However, the code does give an object with enough info to then retrieve the sequences. I edited this code to be able to perform BLASTs in R for a given organism filter. The returned object gives gene ids and definitions.

You can find my cleaned and edited code is here

Error in write.table because data.frame contains a list

Filed under: Uncategorized — Tags: , , , — S @ 06:42

Error in .External2(C_writetable, x, file, nrow(x), p, rnames, sep, eol, :
unimplemented type 'list' in 'EncodeElement'

I got this error when trying to write a table write.table on an object. The object was a data.frame but one of the elements was a list (it is unclear why it was a list, just R magic). The simplest workaround is to convert the data.frame to a matrix as.matrix and save that object with write.table

Older Posts »

Create a free website or blog at WordPress.com.