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<h1 class="title toc-ignore">Inspect samples detected as absent or not having a nucleus</h1>
<h4 class="author"><em>Joyce Hsiao</em></h4>
</div>
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<p><strong>Last updated:</strong> 2017-12-11</p>
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<p><strong>Code version:</strong> 397a117</p>
<div id="load-packages-and-data" class="section level2">
<h2>Load packages and data</h2>
<pre class="r"><code>library(knitr)</code></pre>
<p>Load nuclei detection results directly from image analysis output <code>/project2/gilad/fucci-seq/intensities</code>. The results are made into a summary table.</p>
<p><code>plate</code>: labeled by the mix of individual cell lines<br />
<code>image</code>: labels assigned by the JULI imaging system. These will be converted to correspond to C1 plate labels (rows and columns).<br />
<code>nnuclei</code>: number of nuclei detected in a single cell sample</p>
<pre class="r"><code>fls <- list.files("/project2/gilad/fucci-seq/intensities", pattern = "rds", full.names = TRUE)
nuclei_table <- do.call(rbind, lapply(1:length(fls), function(index) {
tmp <- readRDS(fls[[index]])
plate <- strsplit(strsplit(fls[index], split="/")[[1]][[6]],
split=".", fixed = TRUE)[[1]][[1]]
data.frame(plate=plate, nnuclei=tmp, image=names(tmp))
}))
saveRDS(nuclei_table, "/project2/gilad/joycehsiao/fucci-seq/output/image-qc.rds")</code></pre>
<p>Inspect samples</p>
<pre class="r"><code>nuclei_table <- readRDS("/project2/gilad/joycehsiao/fucci-seq/output/image-qc.rds")
kable(nuclei_table[which(nuclei_table$nnuclei==0|is.na(nuclei_table$nnuclei)),])</code></pre>
<table>
<thead>
<tr class="header">
<th></th>
<th align="left">plate</th>
<th align="right">nnuclei</th>
<th align="left">image</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td>00010</td>
<td align="left">18511_18855</td>
<td align="right">NA</td>
<td align="left">00010</td>
</tr>
<tr class="even">
<td>00048</td>
<td align="left">18511_18855</td>
<td align="right">NA</td>
<td align="left">00048</td>
</tr>
<tr class="odd">
<td>000071</td>
<td align="left">18855_19098</td>
<td align="right">NA</td>
<td align="left">00007</td>
</tr>
<tr class="even">
<td>000481</td>
<td align="left">18855_19098</td>
<td align="right">NA</td>
<td align="left">00048</td>
</tr>
<tr class="odd">
<td>000712</td>
<td align="left">18855_19101</td>
<td align="right">NA</td>
<td align="left">00071</td>
</tr>
<tr class="even">
<td>000882</td>
<td align="left">18855_19101</td>
<td align="right">NA</td>
<td align="left">00088</td>
</tr>
<tr class="odd">
<td>000463</td>
<td align="left">18855_19160</td>
<td align="right">NA</td>
<td align="left">00046</td>
</tr>
<tr class="even">
<td>000164</td>
<td align="left">18870_18511</td>
<td align="right">0</td>
<td align="left">00016</td>
</tr>
<tr class="odd">
<td>000314</td>
<td align="left">18870_18511</td>
<td align="right">NA</td>
<td align="left">00031</td>
</tr>
<tr class="even">
<td>000324</td>
<td align="left">18870_18511</td>
<td align="right">NA</td>
<td align="left">00032</td>
</tr>
<tr class="odd">
<td>000604</td>
<td align="left">18870_18511</td>
<td align="right">NA</td>
<td align="left">00060</td>
</tr>
<tr class="even">
<td>000684</td>
<td align="left">18870_18511</td>
<td align="right">NA</td>
<td align="left">00068</td>
</tr>
<tr class="odd">
<td>000844</td>
<td align="left">18870_18511</td>
<td align="right">NA</td>
<td align="left">00084</td>
</tr>
<tr class="even">
<td>000165</td>
<td align="left">18870_18855</td>
<td align="right">NA</td>
<td align="left">00016</td>
</tr>
<tr class="odd">
<td>000785</td>
<td align="left">18870_18855</td>
<td align="right">NA</td>
<td align="left">00078</td>
</tr>
<tr class="even">
<td>000096</td>
<td align="left">18870_19101</td>
<td align="right">NA</td>
<td align="left">00009</td>
</tr>
<tr class="odd">
<td>000666</td>
<td align="left">18870_19101</td>
<td align="right">NA</td>
<td align="left">00066</td>
</tr>
<tr class="even">
<td>000756</td>
<td align="left">18870_19101</td>
<td align="right">NA</td>
<td align="left">00075</td>
</tr>
<tr class="odd">
<td>000177</td>
<td align="left">18870_19160</td>
<td align="right">NA</td>
<td align="left">00017</td>
</tr>
<tr class="even">
<td>000529</td>
<td align="left">19098_18870</td>
<td align="right">NA</td>
<td align="left">00052</td>
</tr>
<tr class="odd">
<td>0000710</td>
<td align="left">19098_19160</td>
<td align="right">NA</td>
<td align="left">00007</td>
</tr>
<tr class="even">
<td>0002010</td>
<td align="left">19098_19160</td>
<td align="right">NA</td>
<td align="left">00020</td>
</tr>
<tr class="odd">
<td>0002610</td>
<td align="left">19098_19160</td>
<td align="right">NA</td>
<td align="left">00026</td>
</tr>
<tr class="even">
<td>0004910</td>
<td align="left">19098_19160</td>
<td align="right">NA</td>
<td align="left">00049</td>
</tr>
<tr class="odd">
<td>0008410</td>
<td align="left">19098_19160</td>
<td align="right">0</td>
<td align="left">00084</td>
</tr>
<tr class="even">
<td>0004211</td>
<td align="left">19101_18511</td>
<td align="right">NA</td>
<td align="left">00042</td>
</tr>
<tr class="odd">
<td>0005411</td>
<td align="left">19101_18511</td>
<td align="right">NA</td>
<td align="left">00054</td>
</tr>
<tr class="even">
<td>0005611</td>
<td align="left">19101_18511</td>
<td align="right">NA</td>
<td align="left">00056</td>
</tr>
<tr class="odd">
<td>0001613</td>
<td align="left">19101_19160</td>
<td align="right">NA</td>
<td align="left">00016</td>
</tr>
<tr class="even">
<td>0002513</td>
<td align="left">19101_19160</td>
<td align="right">NA</td>
<td align="left">00025</td>
</tr>
<tr class="odd">
<td>0002613</td>
<td align="left">19101_19160</td>
<td align="right">NA</td>
<td align="left">00026</td>
</tr>
<tr class="even">
<td>0002813</td>
<td align="left">19101_19160</td>
<td align="right">NA</td>
<td align="left">00028</td>
</tr>
<tr class="odd">
<td>0003313</td>
<td align="left">19101_19160</td>
<td align="right">NA</td>
<td align="left">00033</td>
</tr>
<tr class="even">
<td>0003015</td>
<td align="left">19160_18870</td>
<td align="right">0</td>
<td align="left">00030</td>
</tr>
<tr class="odd">
<td>0003215</td>
<td align="left">19160_18870</td>
<td align="right">0</td>
<td align="left">00032</td>
</tr>
</tbody>
</table>
<hr />
</div>
<div id="printing-images-for-inspection" class="section level2">
<h2>Printing images for inspection</h2>
<p><strong>This section is for record keeping. All images for samples with no nucleus detected have been converted to PNG format and stored in /project2/gilad/fucci-seq/images-inspect-zero-nucleus.</strong></p>
<p>The code below will save images in png format at <code>/project2/gilad/fucci-seq/images-inspect-zero-nucleus</code>.</p>
<pre class="r"><code>#' @param wells vector of wells ID (use the format specified above).
#' @param plate plate ID
print_png <- function(plate, wells) {
for (index in 1:length(wells)) {
id <- wells[index]
dir_images_data_pl <- paste0("/project2/gilad/fucci-seq/images_curated/",plate,"/")
dir_output <- "/project2/gilad/fucci-seq/images-inspect-zero-nucleus/"
bright <- readImage(paste0(dir_images_data_pl, "BRIGHT/", id, ".TIFF"))
dapi <- readImage(paste0(dir_images_data_pl, "DAPI/", id, ".TIFF"))
gfp <- readImage(paste0(dir_images_data_pl, "GFP/", id, ".TIFF"))
rfp <- readImage(paste0(dir_images_data_pl, "RFP/", id, ".TIFF"))
writeImage(bright, paste0(dir_output, plate,".",id,".bright.png"))
writeImage(dapi, paste0(dir_output, plate,".",id,".dapi.png"))
writeImage(gfp, paste0(dir_output, plate,".",id,".gfp.png"))
writeImage(rfp, paste0(dir_output, plate,".",id,".rfp.png"))
# combo <- combine(dapi, bright, gfp, rfp)
# writeImage(combo, paste0(dir_output, plate,".",id,".combo.png"))
}
}
tmp_table <- nuclei_table[which(nuclei_table$nnuclei == 0 | is.na(nuclei_table$nnuclei)),]
plates <- unique(as.character(tmp_table$plate))
for (index in 1:length(plates)) {
plate <- plates[index]
cases <- nuclei_table[which( (nuclei_table$nnuclei == 0 | is.na(nuclei_table$nnuclei)) & nuclei_table$plate == plate),]
wells <- as.character(cases$image)
print_png(plate, wells)
}</code></pre>
</div>
<div id="manaul-inspection" class="section level2">
<h2>Manaul inspection</h2>
<p>18855_19101.00071 : 1 18855_19101.00088 : 1 18855_19160.00046 : 1 18870_18511.00016 : 1 18870_18511.00032 : 1 18870_18511.00068 : 1 18870_18511.00084 : 1 18870_18855.00016 : 1 18870_18855.00078 : 1 18870_19101.00066 : 1 18870_19101.00075 : 1 19098_18870.00052 : 1 19098_19160.00020 : 1 19098_19160.00049 : 1 19098_19160.00084 : 1 19101_18511.00042 : 1 19101_18511.00054 : 1 19101_19160.00016 : 1 19101_19160.00026 : 1 19101_19160.00033 : 1</p>
<hr />
</div>
<div id="session-information" class="section level2">
<h2>Session information</h2>
<pre class="r"><code>sessionInfo()</code></pre>
<pre><code>R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.2 (Nitrogen)
Matrix products: default
BLAS: /home/jdblischak/software/miniconda3/envs/fucci-seq/lib/R/lib/libRblas.so
LAPACK: /home/jdblischak/software/miniconda3/envs/fucci-seq/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.16
loaded via a namespace (and not attached):
[1] compiler_3.4.1 backports_1.0.5 magrittr_1.5 rprojroot_1.2
[5] tools_3.4.1 htmltools_0.3.6 yaml_2.1.14 Rcpp_0.12.13
[9] stringi_1.1.2 rmarkdown_1.6 highr_0.6 git2r_0.19.0
[13] stringr_1.2.0 digest_0.6.12 evaluate_0.10.1</code></pre>
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