ComplexHeatmap - Highlight specific values in a heatmap - r

I'm using the ComplexHeatmap package in R to plot a matrix.
I would like to plot cells with specific values in different colors such as:
Red if value < threshold_low
Yellow if threshold_low < value < threshold_high
Green gradient if threshold_high < value < 0.9
White if value > 0.9
The code below produces something close to what I'm trying to achieve but not exactly...
There should be 3 values highlighted in 'red' (only are shown).
The legend doesn't show the red value.
I've tried different values in colorRamp2() but I still achieve the results I want.
Link to the package: https://github.com/jokergoo/ComplexHeatmap
Relevant documentation: https://bioconductor.statistik.tu-dortmund.de/packages/3.1/bioc/vignettes/ComplexHeatmap/inst/doc/ComplexHeatmap.html
Reproducible example:
library(ComplexHeatmap)
library(circlize)
library(RColorBrewer)
mat <- structure(c(1, 0.154616894313456, 0.168336307012768, 1, 1, 0.453975613676526,
1, 1, 1, 1, 0.00056792615275985, 1, 1, 1, 1, 1, 0.105149642433548,
0.425158360263792, 1, 1, 0.501057722133202, 1, 1, 1, 0.00278294210196398,
1, 0.168271031634512, 1, 0.830063213792425, 1, 1, 1, 1, 1, 1,
1, 1, 1, 0.451156419955746, 1, 0.0274775797365075, 1, 1, 0.717017044202449,
1, 1, 1, 0.717321290931695, 0.0845704812428829, 1, 0.0699956751028108,
1, 0.275329648641519, 1, 0.0201980178890521, 0.0455613967501329,
1, 1, 0.536035636664544, 1, 1, 1, 1, 0.358910397894989, 1, 1,
1, 1, 1, 0.0467579359404697, 0.100390014456881, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 0.00196501415273741, 1, 1, 1, 1, 1, 1, 1, 1, 1,
0.52718575076658, 0.589648919728843, 0.016642521684359, 1, 1,
0.100523837174713, 0.62858401844093, 1, 1, 1, 0.00272095544860866,
1, 0.00152884219028376, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.00715615768151061,
1, 1, 0.0017044025565658, 1, 0.900838683850751, 1, 0.00286177891699905,
0.964009307250068, 1, 1, 1, 1, 0.712505373834541, 0.156595117903911,
0.698630689400136, 0.0497797620046933, 0.0432669236844255, 1,
0.482930753871518, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.863198034258964,
0.0914794415922655, 1, 1, 1, 1, 1, 0.130770966476073, 0.133939889164611,
1, 0.357244624441367, 0.0574932940137384, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 0.10152332525958, 1, 1, 1, 1, 1, 1, 1,
0.613891861387759, 1, 1, 1, 1, 0.0194347260355869, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.836989723814452,
0.262496570009738, 0.0266926025635128, 1, 1, 1, 0.409918984740791,
1, 1, 1, 0.000826603369076878, 0.251385649690035, 0.262496570009738,
1, 0.636285376736921, 1, 1, 1, 0.131975914025068, 1, 0.302372382987271,
1, 0.829657680365184, 0.234804722298138, 1, 0.480189087472427,
1, 1, 0.434351639718704, 1, 1, 1, 1, 1, 1, 1, 1, 0.827162805570832,
1, 0.000754621951469572, 1, 1, 1, 0.0607557227589793, 0.0466844602596043,
0.166584131048057, 1, 0.00375850252234914, 1, 0.00714919767503871,
1, 1, 0.0274923567061487, 0.317749204479313, 0.523992490899291,
0.0154308196673378, 1, 1, 1, 1, 0.283874713710679, 1, 1, 0.0879611832530085,
0.00614031465663928, 1, 0.44858333972042, 1, 1, 1, 1, 1, 1, 0.0999740979976858,
1, 0.0857648171802508, 0.129753363733359, 0.205913325652849,
0.164132124317898, 1, 1, 0.135339969223928, 0.441555384681617,
1, 1, 1, 0.619544298689775, 1, 1, 1, 1, 1, 0.00237701375005596,
1, 1, 0.149979241487463, 5.65028970245137e-06, 0.00435404367430347,
0.102437190438328, 0.159652054514079, 1.34807420832168e-05, 0.0781174367417338,
0.00168329325806749, 1, 1, 0.0178846842165573, 0.562000511433683,
1, 0.226033494133538, 1, 1, 1, 0.0116432115170938, 0.0158685033438527,
1, 1, 1, 1, 1, 0.226315459031352, 1, 0.0839844171448521, 0.00448638209236464,
0.741937003903222, 1, 1, 0.0969877781197935, 1, 1, 0.899533885687393,
0.11038695014775, 0.0691406897023532, 0.00864645807981477, 0.000409055625639548,
0.0432931123545735, 0.000183686382465392, 1, 1, 1, 1, 1, 0.262742531844371,
1, 0.695486348184785, 0.129359897480463, 0.7456928940893, 0.85934081881042,
1, 1, 1, 1, 1, 0.608552296219399, 1, 0.39067450494575, 1, 1,
1, 1, 0.411281105041672, 0.484196212791728, 0.198292538014945,
0.677053068881975, 1, 1, 1, 0.0318317218601013, 1, 1, 0.791347998335414,
1, 1, 1, 1, 0.240600397196919, 0.135644227364626, 1, 1, 1, 8.78013264925257e-05,
0.259727834661945, 0.305025003277675, 0.0492101609648877, 1,
0.667608208227447, 0.15068985721195, 1, 0.00197605148651341,
0.194624037083573, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0.0758606965055501,
1, 1, 1, 1, 0.146826771370067, 1, 0.0318317218601013, 1, 0.267193726901327,
1, 0.0214353975572249, 1, 1), .Dim = c(53L, 8L), .Dimnames = list( NULL, NULL))
threshold_low <- 0.00015
threshold_high <- 0.05
color_breaks <-c(0, threshold_low, threshold_high, 0.9)
my_palette <- c( "red",
"yellow",
colorRampPalette(rev(brewer.pal(8, "Greens")))(n = length(color_breaks)-3),
"white")
col_fun = colorRamp2(color_breaks, my_palette)
Heatmap(mat,
cluster_rows = FALSE,
show_column_names = FALSE, # We use colored anno_block instead
#clustering_distance_rows = "euclidean",
cluster_columns=FALSE,
col = col_fun,
# Legend
heatmap_legend_param = list(
title = "values", direction = "horizontal",
legend_width = unit(.25, "npc"),
at = c(threshold_low, threshold_high, .5),
labels = c("<0.00015" , "<0.05", '1')
),
# Cell separator
rect_gp = gpar(col = "lightgray", lwd = 1),
width=unit(0.6,'npc'),
)


Following is the color mapping function I created:
offset = 1e-10
col_fun = colorRamp2(c(0, 0.00015, 0.00015+offset, 0.05, 0.05+offset, 0.9, 0.9+offset, 1),
c("red", "red", "yellow", "yellow", "lightgreen", "darkgreen", "white", "white"))
The correspondence is
0 "red"
0.00015 "red"
0.00015+offset "yellow"
0.05 "yellow"
0.05+offset "lightgreen"
0.9 "darkgreen"
0.9+offset "white"
1 "white"
The thing is you have different color schema in different intervals, you need to be careful with the endpoints of each interval.

Related

Create groups in data frame based upon whether next value reaches a threshold

I have df with a column diff_index.
I'd like to create a grouping column based on whether the next value is greater than a threshold x - if the next value is greater than x, then I want a new group.
So in this case, if the threshold is 100, the first 12 entries will be group 1, then since the 13th value is 3877, group 2 begins here, until we reach 1979, in which group 3 starts, etc.
A data.table solution would be ideal.
df=structure(list(diff_index = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 3877, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1,
1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1979, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 136, 1, 1, 1, 1, 97, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 2, 11905, 1, 1, 1, 2764, 1, 1, 1, 676, 1, 1, 1, 2,
1, 1, 1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 469, 1, 1,
2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 1, 1, 1,
1, 1, 1, 1, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
8121, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1737, 1, 1, 1, 1, 1, 1, 1,
1, 681, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, NA)), row.names = c(NA,
-393L), class = "data.frame")

library(tidyverse)
df %>%
mutate(group = cumsum(diff_index > 100) + 1)
Or with data.table:
dt[,group:=cumsum(diff_index > 100) + 1]
diff_index group
1: 1 1
2: 1 1
3: 1 1
4: 1 1
5: 1 1
---
389: 1 11
390: 1 11
391: 1 11
392: 1 11
393: NA NA

ggplot line graph shows overlap for discrete Y axis variable

I am trying to plot a time series plot using ggplot. I have a discrete variable that just describes if a vehicle engine was on or off through a given time.
Naturally, it should either be 0 or 1, there can't be an overlap. But as seen in the below plot, there's a considerable overlap.
I am pretty new to ggplot. Could someone please let me know what the issue is.
The code I am using is:
pd %>%
ggplot(aes(x = SampleTime, y = as.factor(Value))) + geom_line(color = 'black') +
labs(x = 'Time', y = 'Ignition Status', title = 'Ignition Status by Time') +
scale_x_datetime(date_breaks = '1 hour', date_labels = '%H') +
theme(axis.title = element_text(size = 18, face = 'bold'),
axis.text = element_text(size = 14, color = 'black'))
structure of data:
str(pd)
'data.frame': 474 obs. of 2 variables:
$ SampleTime: POSIXct, format: "2020-11-30 00:17:46" "2020-11-30 01:17:47" "2020-11-30 02:17:48" "2020-11-30 03:17:49" ...
$ Value : num 0 0 0 0 0 0 0 0 0 1 ...
data used:
structure(list(SampleTime = structure(c(1606675666, 1606679267,
1606682868, 1606686469, 1606690070, 1606693671, 1606697271, 1606700872,
1606704473, 1606706974, 1606707066, 1606707129, 1606707192, 1606707255,
1606707318, 1606707382, 1606707445, 1606707508, 1606707571, 1606707631,
1606707694, 1606707754, 1606707817, 1606707880, 1606707943, 1606708006,
1606708069, 1606708132, 1606708195, 1606708258, 1606708318, 1606708381,
1606708441, 1606708504, 1606708567, 1606708630, 1606708691, 1606708751,
1606708814, 1606708877, 1606708940, 1606709003, 1606709066, 1606709129,
1606709192, 1606709255, 1606709318, 1606709381, 1606709444, 1606709507,
1606709570, 1606709633, 1606709696, 1606709759, 1606709822, 1606709885,
1606709948, 1606710011, 1606710074, 1606710137, 1606710200, 1606710263,
1606710348, 1606710411, 1606710474, 1606710537, 1606710600, 1606710663,
1606710726, 1606710789, 1606710852, 1606710915, 1606710978, 1606711041,
1606711104, 1606711167, 1606711230, 1606711293, 1606711356, 1606711419,
1606711482, 1606711545, 1606711608, 1606711671, 1606711734, 1606711797,
1606711860, 1606711923, 1606711986, 1606712049, 1606712112, 1606712175,
1606712238, 1606712301, 1606712365, 1606712428, 1606712491, 1606712553,
1606712617, 1606712679, 1606712756, 1606712909, 1606712970, 1606713007,
1606713034, 1606713094, 1606713157, 1606713220, 1606713283, 1606713346,
1606713409, 1606713472, 1606713535, 1606713598, 1606713661, 1606713724,
1606713787, 1606713850, 1606713913, 1606713976, 1606714039, 1606714102,
1606714165, 1606714228, 1606714291, 1606714354, 1606714417, 1606714480,
1606714543, 1606714606, 1606714669, 1606714732, 1606714795, 1606714858,
1606714921, 1606714984, 1606715047, 1606715110, 1606715173, 1606715236,
1606715299, 1606715362, 1606715425, 1606715488, 1606715551, 1606715614,
1606715677, 1606715740, 1606715803, 1606715866, 1606715929, 1606715992,
1606716055, 1606716118, 1606716181, 1606716244, 1606716307, 1606716370,
1606716433, 1606716464, 1606716826, 1606716886, 1606716949, 1606717012,
1606717075, 1606717138, 1606717201, 1606717264, 1606717327, 1606717390,
1606717453, 1606717516, 1606717579, 1606717642, 1606717705, 1606717768,
1606717831, 1606717894, 1606717957, 1606718021, 1606718084, 1606718147,
1606718210, 1606718273, 1606718336, 1606718399, 1606718462, 1606718525,
1606718588, 1606718651, 1606718714, 1606718777, 1606718839, 1606718903,
1606718965, 1606719029, 1606719091, 1606719155, 1606719218, 1606719281,
1606719344, 1606719407, 1606719470, 1606719533, 1606719596, 1606719659,
1606719722, 1606719785, 1606719848, 1606719911, 1606719974, 1606720037,
1606720100, 1606720163, 1606720226, 1606720289, 1606720352, 1606720415,
1606720478, 1606720498, 1606721559, 1606721619, 1606721682, 1606721745,
1606721808, 1606721871, 1606721934, 1606721997, 1606722060, 1606722123,
1606722186, 1606722249, 1606722312, 1606722375, 1606722438, 1606722501,
1606722564, 1606722627, 1606722690, 1606722753, 1606722816, 1606722858,
1606722892, 1606722952, 1606723015, 1606723078, 1606723141, 1606723204,
1606723267, 1606723330, 1606723393, 1606723456, 1606723519, 1606723582,
1606723645, 1606723708, 1606723771, 1606723834, 1606723897, 1606723960,
1606724023, 1606724086, 1606724149, 1606724212, 1606724275, 1606724338,
1606724401, 1606724464, 1606724527, 1606724590, 1606724653, 1606724716,
1606724779, 1606724842, 1606724905, 1606724968, 1606725031, 1606725094,
1606725157, 1606725220, 1606725283, 1606725346, 1606725409, 1606725472,
1606725535, 1606725598, 1606725661, 1606725721, 1606725784, 1606725840,
1606729441, 1606730753, 1606730814, 1606730857, 1606731021, 1606731081,
1606731144, 1606731207, 1606731270, 1606731333, 1606731396, 1606731459,
1606731522, 1606731585, 1606731648, 1606731711, 1606731774, 1606731837,
1606731900, 1606731963, 1606732026, 1606732089, 1606732138, 1606732956,
1606733017, 1606733080, 1606733143, 1606733206, 1606733269, 1606733332,
1606733395, 1606733458, 1606733521, 1606733584, 1606733647, 1606733710,
1606733773, 1606733836, 1606733899, 1606733962, 1606734025, 1606734088,
1606734151, 1606734203, 1606735128, 1606735189, 1606735252, 1606735315,
1606735378, 1606735441, 1606735504, 1606735567, 1606735630, 1606735683,
1606739285, 1606742885, 1606744969, 1606745030, 1606745093, 1606745156,
1606745219, 1606745282, 1606745345, 1606745408, 1606745471, 1606745534,
1606745597, 1606745660, 1606745723, 1606745786, 1606745849, 1606745912,
1606745975, 1606746038, 1606746101, 1606746164, 1606746370, 1606746433,
1606746496, 1606746559, 1606746702, 1606746736, 1606746765, 1606746828,
1606746891, 1606746954, 1606747017, 1606747077, 1606747140, 1606747203,
1606747266, 1606747329, 1606747392, 1606747455, 1606747518, 1606747581,
1606747644, 1606747707, 1606747770, 1606747833, 1606747896, 1606747959,
1606748022, 1606748085, 1606748145, 1606748206, 1606748269, 1606748332,
1606748395, 1606748458, 1606748521, 1606748584, 1606748647, 1606748707,
1606748770, 1606748833, 1606748896, 1606748959, 1606749022, 1606749085,
1606749148, 1606749211, 1606749274, 1606749337, 1606749400, 1606749463,
1606749526, 1606749589, 1606749652, 1606749715, 1606749778, 1606749841,
1606749904, 1606749967, 1606750030, 1606750093, 1606750156, 1606750219,
1606750282, 1606750345, 1606750408, 1606750471, 1606750534, 1606750597,
1606750657, 1606750720, 1606750781, 1606750841, 1606750904, 1606750967,
1606751030, 1606751084, 1606754686, 1606758287, 1606759153, 1606759213,
1606759276, 1606759339, 1606759402, 1606759465, 1606759528, 1606759592,
1606759654, 1606759718, 1606759780, 1606759843, 1606759906, 1606759969,
1606760032, 1606760096, 1606760159, 1606760222, 1606760285, 1606760348,
1606760411, 1606760474, 1606760537, 1606760600, 1606760663, 1606760726,
1606760788, 1606760851, 1606760914, 1606760977), class = c("POSIXct",
"POSIXt"), tzone = ""), Value = c(0, 0, 0, 0, 0, 0, 0, 0, 0,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1)), row.names = c(NA, -474L), class = "data.frame")

ggplot automatically connects the gaps between observations if you use geom_line. Try to use geom_point instead to see the gaps:
pd %>%
ggplot(aes(x = SampleTime, y = as.factor(Value))) +
geom_point(color = 'black') +
labs(x = 'Time', y = 'Ignition Status', title = 'Ignition Status by Time') +
scale_x_datetime(date_breaks = '1 hour', date_labels = '%H') +
theme(axis.title = element_text(size = 18, face = 'bold'),
axis.text = element_text(size = 14, color = 'black'))
Alternatively, you can use geom_line but don't convert Value to a factor and use the numeric value instead. This way you can see the change from 0 to 1 more clearly:
pd %>%
ggplot(aes(x = SampleTime, y = Value)) +
geom_line(color = 'black') +
labs(x = 'Time', y = 'Ignition Status', title = 'Ignition Status by Time') +
scale_x_datetime(date_breaks = '1 hour', date_labels = '%H') +
theme(axis.title = element_text(size = 18, face = 'bold'),
axis.text = element_text(size = 14, color = 'black'))
Lastly, a slightly more appropriate option for categorical data might be to use geom_step instead, which at least connects the two categories with a vertical line:
pd %>%
ggplot(aes(x = SampleTime, y = Value)) +
geom_step(color = 'black') +
labs(x = 'Time', y = 'Ignition Status', title = 'Ignition Status by Time') +
scale_x_datetime(date_breaks = '1 hour', date_labels = '%H') +
theme(axis.title = element_text(size = 18, face = 'bold'),
axis.text = element_text(size = 14, color = 'black'))
If that doesn't suffice, check out this post on how to connect the lines between each consecutive dot per group via geom_segment.

How can I write a simple classifier and generate a merged dataframe from it

I have a df like this;
>df[1:6,1:6]
> ABT.263 ABT.869 ABT.888 AC220 Afatinib Afatinib.rescreen.
> BT-20 1 1 1 1 0 1
> CAL-120 0 1 1 1 1 1
> CAL-51 1 1 1 1 1 1
> CAL-85-1 1 1 1 1 1 0
> DU-4475 0 1 1 1 1 1
> HCC1143 1 1 1 1 0 1
Basically, I want to extract 1's and 0's of each column's row name. Then put them into adjacent columns in a loop form.
Desired output is like this;
> final_df[1:6,1:4]
> ABT.263_1 ABT.263_0 ABT.869_1 ABT.869_0
> BT-20 CAL-120 BT-20 NA
> CAL-51 DU-4475 CAL-120
> CAL-85-1 CAL-51
> HCC1143 CAL-85-1
> DU-4475
> HCC1143
I can extract rownames of 0 cells and 1 cells separately with this;
value1 <- rownames(df)[which(df[,1] == 1)]
value0 <- rownames(df)[which(df[,1] == 0)]
However, failed to assign value1 and value0 vectors respectively in a df format with loops.
> dput(head(resp_tnbc, 20))
structure(list(ABT.263 = c(1, 0, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1,
1, 1, 1, 1, 1), ABT.869 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1), ABT.888 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1), AC220 = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 0,
1, 1, 1, 1, 1, 1, 1), Afatinib = c(0, 1, 1, 1, 1, 0, 1, 1, 1,
0, 1, 0, 1, 1, 1, 0, 1), Afatinib.rescreen. = c(1, 1, 1, 0, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), AG.014699 = c(1, 1, 0, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AICAR = c(1, 1, 1, 1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0), AKTinhibitorVIII = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1), AMG.706 = c(1,
1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1), AP.24534 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AR.42 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AS601245 = c(1,
1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AS605240 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AT.7519 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ATRA = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), AUY922 = c(1,
1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AV.951 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), Axitinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0), AZD6244 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), AZD6244.1 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AZD6482 = c(0,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), AZD6482.1 = c(0,
1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), AZD7762 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), AZD8055 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), BAY61.3606 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bexarotene = c(1,
1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bicalutamide = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bicalutamide.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BIRB0796 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0), BIX02189 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bleomycin = c(1,
1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1), Bleomycin.50uM. = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMN.673 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMS.345541 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMS.536924.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMS.708163 = c(1,
0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1), BMS.708163.1 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1), BMS.754807 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bosutinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Bryostatin1 = c(1,
1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), BX.795 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), BX.912 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), CAL.101 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), Camptothecin = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CAY10603 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CCT007093 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CCT018159 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), CEP.701 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Cetuximab = c(0,
1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1), CH5424802 = c(1,
1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0, 0, 1, 0, 1), CHIR.99021 = c(1,
1, 1, 0, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1), CHIR.99021.1 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CI.1040 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Cisplatin = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CP466722 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CP724714 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CUDC.101 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), CX.5461 = c(1,
0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0, 1, 1, 0, 0, 1), Cytarabine = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Dabrafenib = c(1,
0, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), DMOG = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Docetaxel = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Doxorubicin = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), EHT1864 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), EKB.569 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), Elesclomol = c(1,
1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1), Embelin = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), EpothiloneB = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Etoposide = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), EX.527 = c(1,
1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), FH535 = c(1,
1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 0, 0, 1), FK866 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), FMK = c(1, 1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), FR.180204 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), FTI.277 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GDC0941 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), GDC0941.rescreen. = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Gefitinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1), Gemcitabine = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GenentechCpd10 = c(1,
1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GSK.1904529A = c(1,
1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 1, 1, 0, 0, 0, 1), GSK.650394 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GSK1070916 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), GSK2126458 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GSK269962A.1 = c(1,
0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0), GSK429286A = c(1,
1, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), GSK690693 = c(0,
1, 0, 0, 1, 1, 0, 1, 0, 0, 1, 1, 1, 1, 1, 0, 0), GW.2580 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1), GW441756 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0), HG.6.64.1 = c(1,
1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), I.BET151 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), IOX2 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), IPA.3 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JNJ.26854165 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), JNK.9L = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JNKInhibitorVIII = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JQ1 = c(1, 1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JQ1.1 = c(1, 1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1), JQ12 = c(1, 1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), JW.7.24.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.055 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.102 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.236 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.244 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.260 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.266 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KIN001.270 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), KU.55933 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), LAQ824 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Lenalidomide = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), LFM.A13 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), LY317615 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Masitinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Methotrexate = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Midostaurin = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), MitomycinC = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), MK.2206 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0), MLN4924 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), MP470 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), MPS.1.IN.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NG.25 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Nilotinib = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), NPK76.II.72.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NSC.207895 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NSC.87877 = c(1,
0, 0, 0, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), NU.7441 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), Nutlin.3a = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NVP.BEZ235 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), NVP.BHG712 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ObatoclaxMesylate = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Olaparib = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Olaparib.1 = c(1,
0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1), OSI.027 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), OSI.906 = c(1,
1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), OSI.930 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), OSU.03012 = c(1,
1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PAC.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Pazopanib = c(1,
1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1), PD.0325901 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1), PD.0332991 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PD.173074 = c(1,
1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 0), PF.4708671 = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PF.562271 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), PFI.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PHA.793887 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Phenformin = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1), PI.103 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PIK.93 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), piperlongumine = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), PLX4720 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PLX4720.rescreen. = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), PXD101.Belinostat = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), QL.X.138 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), QL.XI.92 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1), QL.XII.47 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), QS11 = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), RDEA119 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), RDEA119.rescreen. = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), RO.3306 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 0, 1), rTRAIL = c(1,
0, 1, 1, 1, 1, 0, 0, 1, 0, 1, 1, 1, 1, 0, 1, 1), Ruxolitinib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SB.505124 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1), SB.715992 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), SB216763 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SB52334 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1), SB590885 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SGC0946 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1), Shikonin = c(1,
1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SL0101.1 = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SN.38 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), SNX.2112 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), STF.62247 = c(1,
1, 1, 1, 0, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), T0901317 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), TAK.715 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Tamoxifen = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Temozolomide = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), Temsirolimus = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), TG101348 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Thapsigargin = c(1,
1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1), THZ.2.102.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), THZ.2.49 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Tipifarnib = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), TL.1.85 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), TL.2.105 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), TPCA.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Trametinib = c(1,
1, 1, 1, 0, 0, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1), TubastatinA = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1), UNC0638 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), UNC0638.1 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), UNC1215 = c(1,
1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Vinblastine = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Vinorelbine = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Vismodegib = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), VNLG.124 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Vorinostat = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), VX.11e = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), VX.702 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), WZ3105 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1), X.5Z..7.Oxozeaenol = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), X17.AAG = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), X5.Fluorouracil = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), X681640 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), XAV939 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0), XL.184 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0), XL.880 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), XMD13.2 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), XMD14.99 = c(1,
1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), XMD15.27 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Y.39983 = c(1,
0, 1, 1, 0, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), YK4.279 = c(1,
1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), YM155 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), YM201636 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), Zibotentan.ZD4054 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ZM.447439 = c(1,
1, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1), ZSTK474 = c(1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1)), row.names = c("BT-20",
"CAL-120", "CAL-51", "CAL-85-1", "DU-4475", "HCC1143", "HCC1187",
"HCC1395", "HCC1937", "HCC2157", "HCC38", "HDQ-P1", "Hs-578-T",
"MDA-MB-231", "MDA-MB-436", "MDA-MB-468", "MFM-223"), class = "data.frame")

Not really sure, because I did not fully understand your desired output...
But here is a go using the data.table-package
#load library
library(data.table)
#first, create the sample data
#note, rownames are stored in their own column, 'row_name'
dt <- fread("row_name ABT.263 ABT.869 ABT.888 AC220 Afatinib Afatinib.rescreen.
BT-20 1 1 1 1 0 1
CAL-120 0 1 1 1 1 1
CAL-51 1 1 1 1 1 1
CAL-85-1 1 1 1 1 1 0
DU-4475 0 1 1 1 1 1
HCC1143 1 1 1 1 0 1")
#melt the data to long format, using the 'row_name'-column as identifier
dt.melt <- melt( dt, id.vars = "row_name" )
#now summarise, pasting together row_names by variable-value combination
dt.melt[, .( row = paste0( row_name, collapse = ";" ) ),
by = .( value = paste0( variable, "_", value ) ) ]
# value row
# 1: ABT.263_1 BT-20;CAL-51;CAL-85-1;HCC1143
# 2: ABT.263_0 CAL-120;DU-4475
# 3: ABT.869_1 BT-20;CAL-120;CAL-51;CAL-85-1;DU-4475;HCC1143
# 4: ABT.888_1 BT-20;CAL-120;CAL-51;CAL-85-1;DU-4475;HCC1143
# 5: AC220_1 BT-20;CAL-120;CAL-51;CAL-85-1;DU-4475;HCC1143
# 6: Afatinib_0 BT-20;HCC1143
# 7: Afatinib_1 CAL-120;CAL-51;CAL-85-1;DU-4475
# 8: Afatinib.rescreen._1 BT-20;CAL-120;CAL-51;DU-4475;HCC1143
# 9: Afatinib.rescreen._0 CAL-85-1

A base R solution with a list of vectors is also possible:
Code:
names <- names(df)
#
l1 <- list()
for(i in 1:length(df)){
l1[[i]] <- rownames(df)[which(df[,names[i]] == 1)]
}
Result
l1
[[1]]
[1] "BT-20" "CAL-51" "CAL-85-1" "HCC1143"
[[2]]
[1] "BT-20" "CAL-120" "CAL-51" "CAL-85-1" "DU-4475" "HCC1143"
[[3]]
[1] "BT-20" "CAL-120" "CAL-51" "CAL-85-1" "DU-4475" "HCC1143"
[[4]]
[1] "BT-20" "CAL-120" "CAL-51" "CAL-85-1" "DU-4475" "HCC1143"
[[5]]
[1] "CAL-120" "CAL-51" "CAL-85-1" "DU-4475"
[[6]]
[1] "BT-20" "CAL-120" "CAL-51" "DU-4475" "HCC1143"
This is the list of names with 1 in the data.frame, the list of 0's could be obtained identically.

Save single data frames found within a list by applying a for loop

I have to work on several data frames to perform the same set of operations. Because of this, I inserted them into a list, and by using lapply I perform some kind of operations.
Then, I want to save each dataframes separately as .txt files, by employing a for loop. Here's the code I wrote:
all <- lapply(names(sampleList),function(mysample){
aux <- read.table(sampleList[[mysample]], col.names=c("Chromosome","Position","Ref_allele","Alt_allele","Fraction","Fw_ref","Rv_ref","Fw_alt","Rv_alt"))
aux <- mutate(aux, ID=paste0(Chromosome, ":", Position)) %>% distinct(ID, .keep_all=T)
})
for( i in 1:length(all))
write.table(all[i], paste0(all[i],"_filtered.txt"))
I would expect to have n new dataframes, named as the original ones + _filtered at the end. But this is what actually happens:
Error in file(file, ifelse(append, "a", "w")) :
cannot open the connection
In addition: Warning message:
In file(file, ifelse(append, "a", "w")) :
cannot open file 'list(Chromosome = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 [... truncated]
But that's not what my data frames contains. By View(as.data.frame(all[n])) I see my data frames looks normal.
Many thanks for any help.

There are a couple things that can be done here:
for( i in 1:length(all))
write.table(all[i], paste0(all[i],"_filtered.txt"))
First, the second argument is supposed to be a string, but your paste0(all[i],...) is working on the frame itself (all[i] is a data.frame embedded in a list of length 1), not the name of it. You might get away with:
for( i in 1:length(all))
write.table(all[i], paste0(names(all)[i], "_filtered.txt"))
But you can continue the theme of "operate on a list of frames" (which is great, btw), by extending your lexicon from just lapply (which executes a function on one vector/list of data) to include Map and mapply, which zips together one or more vectors/lists into individual arguments of a function. Up front:
Map(write.table, all, paste0(names(all), "_filtered.txt"))
should save everything as you intend (and return a list of return values from write.table, which might not be useful).
Explanation: Map(myfun, 1:3, c('a','b','c'), c('X','Y','Z')) is unrolled internally to be
myfun(1, 'a', 'X')
myfun(2, 'b', 'Y')
myfun(3, 'c', 'Z')
So these two are nearly equivalent:
lapply(1:3, myfun)
Map(myfun, 1:3)
(There are some ever-so-minor performance differences between them. If you know you always have one vector, use lapply.)
So to continue a theme of "vectorize as much as you can" (which is a common mantra in R-circles), we generate the filenames early with paste0(names(all), "_filtered.txt"), and then pass two list/vector objects to Map: the list of data, and the file names.

How to plot a different colour depending on the value in geom_line ggplot

I have a ggplot like so:
I would like to have a line that is red if it is above the topmost geom_hline, preferably only when it is above the line. Failing this geom_point colour change will do:
The minimal dataset
structure(list(chr = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1), leftPos = c(480000, 600000, 2520000, 2760000, 2880000,
3000000, 3120000, 3480000, 3600000, 4440000, 5880000, 6120000,
7680000, 8400000, 8520000, 8640000, 8760000, 8880000, 9000000,
9120000, 10320000, 11280000, 12240000, 12360000, 12840000, 13080000,
14760000, 17520000, 17880000, 18120000, 18240000, 18480000, 18600000,
18720000, 19200000, 19320000, 20640000, 21000000, 21120000, 21840000,
22560000, 22680000, 24360000, 24600000, 24720000, 25080000, 25200000,
25440000, 25560000, 25680000, 25920000, 26160000, 26280000, 27000000,
27360000, 27480000, 27840000, 27960000, 28320000, 28440000, 28560000,
28680000, 29160000, 29280000, 29520000, 29760000, 29880000, 30000000,
30120000, 30360000, 30840000, 31200000, 31680000, 32760000, 33000000,
33360000, 33480000, 33600000, 33720000, 33840000, 34080000, 34200000,
34320000, 34440000, 34920000, 35040000, 35160000, 35400000, 35520000,
35640000, 35760000, 35880000, 36000000, 36120000, 36480000, 36720000,
36840000, 37440000, 37680000, 37800000), Means = c(45.1721105399911,
58.3236234466928, 10.701781072969, 81.1844097193854, 15.9764258576336,
72.9857717254786, 100.909692015799, 42.3842652589944, 48.5758167032384,
60.5307788344342, 9.72605226749078, 30.952302909114, 17.860141968134,
30.8530526895484, 20.4628162381967, 116.623581135536, 38.6678878887186,
78.9150157908195, 247.360337239763, 24.8838914877946, 23.429988222356,
53.2615600034024, 52.3424770503346, 170.222454449925, 50.5781138394727,
68.3087962976007, 89.4230029840393, 330.313625666045, 5.03584032143116,
89.2643864875047, 27.8653665885641, 201.299758574135, -5.42494623204948,
46.35601686698, 5.79103997302425, 112.341455197127, -4.28592603543802,
7.41453012965141, 54.7629963052909, 23.3995967033728, 38.50598295151,
51.1117491264575, 9.70064959823299, 145.915122377063, -1.93394721482472,
223.668891284723, 0.967813870514552, 3.98951268889225, 103.991761780532,
25.360339056567, 110.629872488342, 98.3711372064266, 4.29902758331359,
-6.49705043591403, 119.885301893303, 11.7856758287972, 2.14257993846943,
0.895276964913781, -4.13978377824383, 32.8265982947408, 102.894448568246,
16.4150366530933, 3.50639248897849, 96.4740592727108, 163.538533768379,
11.7417544456533, 271.336168593183, 21.9737935918722, 69.3505139183734,
39.0812235546367, -0.0979741416490998, 11.2593492499262, 1.09352485411191,
125.197079877443, 3.72187246405846, 60.0443035930762, 64.269810330157,
16.8509153029321, -1.53165469412626, 17.8174419767041, 12.4924416240186,
77.1154197241883, 50.0459666078323, 44.1948097160243, 7.87958496186204,
24.2661434245405, 36.080204093108, 57.8551517801946, 130.247092097128,
56.2802152403655, 24.1732000185415, 0.805669460114936, 20.805136831573,
89.3895887677943, 12.0889852368913, 189.261728063453, 18.3254402417783,
0.914727515857528, 26.4441526771417, 60.3908804957335)), .Names = c("chr",
"leftPos", "Means"), row.names = c(NA, 100L), class = "data.frame")
The code I am using for one of the plots (facet_wrap comes later)
UL1=400
LL1=0
Median1=200
ggplot(Zoutliers1,aes(x = leftPos,
y = as.numeric(Means),
group = chr,
xend = leftPos,
yend=0))+
#geom_bar(stat="identity",fill = "red", size = 1, colour = "red")+
geom_line()+
#geom_segment(linetype= 1, colour = "#919191")+
#ggtitle(TBBName)+
ylim(-100,480)+
facet_grid(.~chr, space="free_x", scales="free_x")+
geom_hline(yintercept = UL1,size=0.5)+
geom_hline(yintercept = Median1,size=0.5,colour='orange')+
geom_hline(yintercept = LL1,size=0.5)+
theme(panel.margin = unit(0.1, "lines"))+
theme(axis.text.x = element_blank())+
theme(panel.border = element_rect(fill=NA,color="darkred", size=0.5,
linetype="dashed"))+
theme(axis.title = element_blank())

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