Remove an automatic title in a plot (R) - r

I am using a function "lp_lin_panel" from the package "lpirfs", for example:
hor3.1_h <- lp_lin_panel(data_set = panel_3 , data_sample = "Full" , endog_data = "E.tertiary", cumul_mult = TRUE , shock = "lv18_bank_c", diff_shock = FALSE , iv_reg = FALSE , instrum = NULL , panel_model = "within" , panel_effect = "individual" , robust_cov = "vcovSCC" , use_gmm = FALSE, gmm_model = "onestep", gmm_transformation = "d", c_exog_data = cv_3_h, l_exog_data = NULL, confint = 1.96 , hor = 6 )
When I use the command:
plot(hor3.1_h , main = NULL)
I still get an automatic title in the plot. Like this
Is there another way to remove it?
Thank you


Try to use:
plot(hor3.1_h) + labs(title = "")

Related

Add a title to gprofiler2 gosttable in R

Hello I'm a new bioinformatician so bear with me please!
I'm using the gprofiler2 to run GO/KEGG analysis in R using emacs/ess and I want to add a title to the table it offers:
publish_gosttable(gostres, highlight_terms = gostres$result[c(1:2,10,120),],
use_colors = TRUE,
show_columns = c("source", "term_name", "term_size", "intersection_size"),
filename = NULL)
I have tried the title(), tab_header() function but I can't seem to be able to add a title. My question is if there is some other function or package that would allow me to add it instead of having to do it manually.
The code so far
GOresult <- gost(
geneid1up$gene,
organism = "hsapiens",
ordered_query = FALSE,
multi_query = FALSE,
significant = TRUE,
exclude_iea = FALSE,
measure_underrepresentation = FALSE,
evcodes = FALSE,
user_threshold = 0.05,
correction_method = "gSCS",
domain_scope = "annotated",
custom_bg = NULL,
numeric_ns = "",
sources = c("GO:BP","GO:MF","GO:CC","KEGG"),
as_short_link = FALSE)
GOresult1 <- as.data.frame(GOresult$result)
GOresult1$minuslog10pval <- -log10(GOresult1$p_value)
names(GOresult1)[15] <- "-log10(pval)"
GOresult2 <- GOresult1[order(GOresult1$p_value, decreasing=F),]
plot1 <- publish_gosttable(GOresult2, highlight_terms = GOresult2[c(1:20),],
use_colors = FALSE,
show_columns = c("source", "term_name", "term_size", "intersection_size","-log10(pval)"),
filename = NULL)

Does this do the job?
library(gprofiler2)
library(ggplot2)
gostres <- gost(query = c("X:1000:1000000", "rs17396340", "GO:0005005", "ENSG00000156103", "NLRP1"),
organism = "hsapiens", ordered_query = FALSE,
multi_query = FALSE, significant = TRUE, exclude_iea = FALSE,
measure_underrepresentation = FALSE, evcodes = FALSE,
user_threshold = 0.05, correction_method = "g_SCS",
domain_scope = "annotated", custom_bg = NULL,
numeric_ns = "", sources = NULL, as_short_link = FALSE)
publish_gosttable(gostres, highlight_terms = gostres$result[c(1:2,10,120),],
use_colors = TRUE,
show_columns = c("source", "term_name", "term_size", "intersection_size"),
filename = NULL)+
ggtitle('Your Title')
Result:
The trick is that the plot is a ggplot objet. Therefore you can add the title using +ggtitle('Your Title') after your plot code (as in my example)

How to use set_token in mapdeck?

I'm trying to reproduce this example: https://github.com/SymbolixAU/mapdeck, using mapdeck r package.
I registered myself on mapbox site and create my token.
Whenever I run my script there is no error, but there is no map either.
library(mapdeck)
library(leaflet)
key <- set_token("pk.eyJ1IjoicmFxdWVsc2FyYWl2YTE5ODgiLCJhIjoiY2p4MzM2eHh5MG95aTN5cDQxdjVocDlxMCJ9.Wskus8QqYwjAufGpW71OVg")
df <- readRDS("df.rds")
df$Station_Long = as.numeric(as.character(df$lon_Pay))
df$Station_Lat = as.numeric(as.character(df$lat_Pay))
df$id = as.factor(as.numeric(as.factor(df$ID)))
mapdeck(
token = key,
style = mapdeck_style('dark')
, location = c(104, 1)
, zoom = 8
, pitch = 45
) %>%
add_arc(
data = df
, origin = c("centroid_lon", "centroid_lat")
, destination = c("lon_Pay", "lat_Pay")
, layer_id = 'arclayer'
, stroke_width = 3
, stroke_from = "#ccffff"
, stroke_to = "#ccffff"
)
My key is NULL (empty).
Does anybody knows why this is happening?

If you use set_token() you don't assign it to a variable, you just call it.
library(mapdeck)
set_token( "YOUR_MAPOBX_TOKEN" )
It's then stored globally in your session
## view your token
mapdeck_tokens()
# Mapdeck tokens
# - mapbox : YOUR_MAPBOX_TOKEN
Using set_token() means you don't have to supply the token argument in the mapdeck() call
url <- 'https://raw.githubusercontent.com/plotly/datasets/master/2011_february_aa_flight_paths.csv'
flights <- read.csv(url)
flights$id <- seq_len(nrow(flights))
flights$stroke <- sample(1:3, size = nrow(flights), replace = T)
flights$info <- paste0("<b>",flights$airport1, " - ", flights$airport2, "</b>")
mapdeck( style = mapdeck_style("dark"), pitch = 45 ) %>%
add_arc(
data = flights
, layer_id = "arc_layer"
, origin = c("start_lon", "start_lat")
, destination = c("end_lon", "end_lat")
, stroke_from = "airport1"
, stroke_to = "airport2"
, stroke_width = "stroke"
, tooltip = "info"
, auto_highlight = TRUE
, legend = T
, legend_options = list(
stroke_from = list( title = "Origin airport" ),
css = "max-height: 100px;")
)

Create a script with 2 vectors in R

I'm using Heatmap from the package complexheatmap
in the script, I need to create a variable ha_column that I will incorporate into my script.
ha_column = HeatmapAnnotation (df = data.frame(type1=c(rep("name1",5), rep("name2",5),rep("name3",5), col = list(type1=c("name1" = "#DCDCDC", "name2" = "#DC928B", "name2"="#BA72D3")))))
I have 2 vectors:
vectors1=c("name1","name2","name3)
vectors2=c("#DCDCDC","#DC928B","#BA72D3")
and the idea is to reproduce the above script with these two vectors.
I tried:
paste0("ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep(",vectors1,", 5),col = list(type1 = c(",vectors1,"=",vectors2,")))")
bu it only paste line by line such as:
[1] "ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep(name1, 5),col = list(type1 = c(name1=#DCDCDC)))"
[2] "ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep(name2, 5),col = list(type1 = c(name2=#DC928B)))"
[3] "ha_column = HeatmapAnnotation(df = data.frame(type1 = c(rep(name3, 5),col = list(type1 = c(name3=#BA72D3)))"
instead of doing what I want ...
Does anyone have an idea?
Thanks for your time.

It's generally not a good idea to build code as a string. Instead think of building a function to do what you want.
You could do something line
ha_column_fun = function(names, colors) {
HeatmapAnnotation(
df = data.frame(type1 = rep(names, each=5)),
col = list(type1=setNames(colors, names))
)
}
And then you could call it with
ha_column = ha_column_fun(vectors1, vectors2)

how to write in xlsx and modifying the format of the cells

After running this code
library(XLConnect)
template <- loadWorkbook ( filename = "template.xlsx" , create = T )
createSheet ( template , c("sheet1","sheet2") )
# setStyleAction(template,XLC$"STYLE_ACTION.NONE")
Data <- data.frame(
a = 1:10,
b = 11:20
)
setDataFormatForType(template, type = XLC$DATA_TYPE.NUMERIC, format = "0.00" )
# list22$`Brand Equity` <- as.numeric(list22$`Brand Equity`)
# list22$`Purchase Intent` <- as.numeric(list22$`Purchase Intent`)
csHeader <- createCellStyle(template, name = "header10")
setFillPattern(csHeader, fill = XLC$BORDER.DOUBLE)
setFillForegroundColor(csHeader, color = XLC$COLOR.DARK_RED)
# setCellFormula(object = template, sheet = (paste0("sheet",i)), row = c(2:4),col = c(1:3), formula = )
setCellStyle(template, sheet = "sheet1", row = 1,
col = c(1:2), cellstyle = csHeader)
setCellStyle(template, sheet = "sheet2", row = 1,
col = c(1:2), cellstyle = csHeader)
for (i in 1:2)
{
setColumnWidth(template, sheet = (paste0("sheet",i)), column = c(1:3), width = 15800)
writeWorksheet ( template , data = Data, sheet = (paste0("sheet",i)), startRow = 1 , startCol = 1 ,
header = TRUE )
}
saveWorkbook ( template )
I obtain
and
It does not seem to pass my argument about the color of the cell. Any ideas ? Moreover is there a way to write transform the numbers in percentages ? So 1 for instance would be 100%, 2 would be 200% etc...

For converting the numbers into percentage, you can write a function similar to this one:
addformatperc<-function(num,roundlevel){
betternum<-paste(prettyNum(round(num*100,roundlevel),big.mark = ","),"%",sep="")
return(betternum)
}
#Output
addformatperc(1,0)
[1] "100%"

Retrieve the position (column name) of the maximum value of the derivative of an interval

To calculate the Red Edge Position Index, I need to find the wavelength value (column name) corresponding to the maximum derivative of reflectance in the red edge region from 690nm to 740nm. I have included a subset of my dataframe below, it contains the correct interval...
I have 640 rows (Sample) of 2151 measurements (values) plus a few catagoricals in the first columns (e.g. plantType and plantCondition). I need to find the column of the value corresponding to the maximum of the derivative of the values in the interval specified and return the wavelength value to the REPI column.
I am trying something like this but I do not know how to calculate the maximum of the derivative in the specified interval
# find the maximum of the derivative of the values in columns x690:x740
# attempt to find for single sample first
> which( colnames(spec.data)=="X690")
[1] 352
> which( colnames(spec.data)=="X740")
[1] 402
# I want to return the values of the differential but this doesn't work
> foo.vector <- diff(spec.data[1,352:402])
>> Error in r[i1] - r[-length(r):-(length(r) - lag + 1L)] : non-numeric argument to binary operator
This makes sense because I don't have the dt in dx/dt but I am not sure how to retrieve the position of the maximum value of the derivative of this interval. once I did I think I would
> spec.data$REPI <- which( colnames(spec.data) == max(foo.vector))
Then I think I would lapply this for each row?
Can anyone point me towards a solution for this?
Thank you...
subset of data from dput
> dput(spec.data[1:2, c(1:3, 7, 300:450)])
structure(list(Sample = c("JUMO_G1 P1T9 Leaf Clip00000.asd",
"JUMO_G1 P1T9 Leaf Clip00001.asd"), plantType = c("JUMO", "JUMO"
), plantCondition = c("G", "G"), REPI = c(NA_real_, NA_real_),
X638 = c(0.0611, 0.06114), X639 = c(0.0606, 0.06064), X640 = c(0.0601,
0.06012), X641 = c(0.0595, 0.05953), X642 = c(0.0589, 0.05893
), X643 = c(0.0584, 0.05834), X644 = c(0.0577, 0.05775),
X645 = c(0.05717, 0.05717), X646 = c(0.0566, 0.05664), X647 = c(0.0562,
0.05618), X648 = c(0.0557, 0.05573), X649 = c(0.0554, 0.05536
), X650 = c(0.0551, 0.05505), X651 = c(0.0547, 0.05475),
X652 = c(0.05448, 0.05447), X653 = c(0.0542, 0.05421), X654 = c(0.054,
0.05395), X655 = c(0.0536, 0.05357), X656 = c(0.0532, 0.05319
), X657 = c(0.0528, 0.05277), X658 = c(0.0523, 0.05229),
X659 = c(0.0518, 0.05176), X660 = c(0.05128, 0.05126), X661 = c(0.0508,
0.05077), X662 = c(0.0503, 0.05024), X663 = c(0.0498, 0.04978
), X664 = c(0.0494, 0.04936), X665 = c(0.049, 0.04897), X666 = c(0.04869,
0.04866), X667 = c(0.0484, 0.04838), X668 = c(0.0482, 0.04815
), X669 = c(0.048, 0.04797), X670 = c(0.0479, 0.04782), X671 = c(0.0478,
0.04775), X672 = c(0.0478, 0.04773), X673 = c(0.0478, 0.04773
), X674 = c(0.0478, 0.04776), X675 = c(0.0479, 0.04786),
X676 = c(0.0481, 0.04802), X677 = c(0.0483, 0.0482), X678 = c(0.0486,
0.04843), X679 = c(0.0489, 0.04873), X680 = c(0.04925, 0.04911
), X681 = c(0.0498, 0.04962), X682 = c(0.0504, 0.05026),
X683 = c(0.05122, 0.05103), X684 = c(0.0522, 0.052), X685 = c(0.0533,
0.05317), X686 = c(0.0548, 0.05458), X687 = c(0.05647, 0.05627
), X688 = c(0.0584, 0.05824), X689 = c(0.0608, 0.06057),
X690 = c(0.0634, 0.06326), X691 = c(0.0664, 0.06626), X692 = c(0.0698,
0.06958), X693 = c(0.0734, 0.07317), X694 = c(0.0773, 0.07701
), X695 = c(0.0814, 0.08109), X696 = c(0.0856, 0.0854), X697 = c(0.0901,
0.08989), X698 = c(0.0947, 0.09449), X699 = c(0.0994, 0.09917
), X700 = c(0.10417, 0.10395), X701 = c(0.10899, 0.10881),
X702 = c(0.11385, 0.11366), X703 = c(0.11871, 0.11854), X704 = c(0.12356,
0.12342), X705 = c(0.1284, 0.12829), X706 = c(0.13324, 0.13312
), X707 = c(0.13803, 0.13792), X708 = c(0.14281, 0.14273),
X709 = c(0.14763, 0.14755), X710 = c(0.15243, 0.15235), X711 = c(0.15718,
0.15713), X712 = c(0.16192, 0.16189), X713 = c(0.1667, 0.16663
), X714 = c(0.17143, 0.17137), X715 = c(0.17609, 0.17605),
X716 = c(0.18069, 0.18062), X717 = c(0.18528, 0.1852), X718 = c(0.18977,
0.18968), X719 = c(0.19417, 0.19406), X720 = c(0.19851, 0.19838
), X721 = c(0.20276, 0.20263), X722 = c(0.20686, 0.20671),
X723 = c(0.2108, 0.21063), X724 = c(0.21465, 0.21449), X725 = c(0.21837,
0.21819), X726 = c(0.22194, 0.22174), X727 = c(0.22534, 0.22515
), X728 = c(0.2286, 0.22838), X729 = c(0.23164, 0.23142),
X730 = c(0.23447, 0.23427), X731 = c(0.23719, 0.23696), X732 = c(0.23984,
0.23959), X733 = c(0.24229, 0.24203), X734 = c(0.24452, 0.24426
), X735 = c(0.24668, 0.24638), X736 = c(0.24867, 0.24839),
X737 = c(0.25053, 0.25028), X738 = c(0.25229, 0.25203), X739 = c(0.25382,
0.25359), X740 = c(0.25531, 0.25508), X741 = c(0.25672, 0.25646
), X742 = c(0.25791, 0.25766), X743 = c(0.25907, 0.25884),
X744 = c(0.26014, 0.25993), X745 = c(0.2611, 0.26089), X746 = c(0.26201,
0.26178), X747 = c(0.26278, 0.26257), X748 = c(0.26347, 0.26329
), X749 = c(0.26414, 0.26397), X750 = c(0.26475, 0.26459),
X751 = c(0.26525, 0.2651), X752 = c(0.26568, 0.26554), X753 = c(0.26614,
0.266), X754 = c(0.26652, 0.26639), X755 = c(0.26682, 0.26671
), X756 = c(0.2671, 0.26701), X757 = c(0.26743, 0.26734),
X758 = c(0.26767, 0.26758), X759 = c(0.26789, 0.26781), X760 = c(0.26814,
0.26808), X761 = c(0.2682, 0.26817), X762 = c(0.26835, 0.26831
), X763 = c(0.26856, 0.26851), X764 = c(0.26872, 0.26869),
X765 = c(0.26884, 0.26881), X766 = c(0.26892, 0.2689), X767 = c(0.26896,
0.26894), X768 = c(0.26898, 0.26896), X769 = c(0.2691, 0.26909
), X770 = c(0.2692, 0.2692), X771 = c(0.26921, 0.26921),
X772 = c(0.26923, 0.26926), X773 = c(0.26927, 0.26931), X774 = c(0.26935,
0.26939), X775 = c(0.26945, 0.26947), X776 = c(0.26946, 0.26949
), X777 = c(0.26948, 0.26952), X778 = c(0.26953, 0.26958),
X779 = c(0.26958, 0.26963), X780 = c(0.26965, 0.2697), X781 = c(0.2697,
0.26975), X782 = c(0.2697, 0.26977), X783 = c(0.26972, 0.26978
), X784 = c(0.26979, 0.26982), X785 = c(0.26987, 0.2699),
X786 = c(0.26991, 0.26998), X787 = c(0.26989, 0.26997), X788 = c(0.26991,
0.26998)), .Names = c("Sample", "plantType", "plantCondition",
"REPI", "X638", "X639", "X640", "X641", "X642", "X643", "X644",
"X645", "X646", "X647", "X648", "X649", "X650", "X651", "X652",
"X653", "X654", "X655", "X656", "X657", "X658", "X659", "X660",
"X661", "X662", "X663", "X664", "X665", "X666", "X667", "X668",
"X669", "X670", "X671", "X672", "X673", "X674", "X675", "X676",
"X677", "X678", "X679", "X680", "X681", "X682", "X683", "X684",
"X685", "X686", "X687", "X688", "X689", "X690", "X691", "X692",
"X693", "X694", "X695", "X696", "X697", "X698", "X699", "X700",
"X701", "X702", "X703", "X704", "X705", "X706", "X707", "X708",
"X709", "X710", "X711", "X712", "X713", "X714", "X715", "X716",
"X717", "X718", "X719", "X720", "X721", "X722", "X723", "X724",
"X725", "X726", "X727", "X728", "X729", "X730", "X731", "X732",
"X733", "X734", "X735", "X736", "X737", "X738", "X739", "X740",
"X741", "X742", "X743", "X744", "X745", "X746", "X747", "X748",
"X749", "X750", "X751", "X752", "X753", "X754", "X755", "X756",
"X757", "X758", "X759", "X760", "X761", "X762", "X763", "X764",
"X765", "X766", "X767", "X768", "X769", "X770", "X771", "X772",
"X773", "X774", "X775", "X776", "X777", "X778", "X779", "X780",
"X781", "X782", "X783", "X784", "X785", "X786", "X787", "X788"
), row.names = 1:2, class = "data.frame")

You can try this
spec.data$REPI <- apply(spec.data[,-(1:4)], 1, function(x) which.max(diff(x)))
Or you can try using dplyr and tidyr:
library(dplyr)
library(tidyr)
spec.data %>%
gather(key, value, -Sample, -plantType, - plantCondition, -REPI) %>%
group_by(Sample) %>%
summarise(which.max(diff(value)))
They both seem to give same results.

Resources