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change panel tabset in qc.qmd #28

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10 changes: 8 additions & 2 deletions 01_quality_assessment/scRNA_QC.qmd
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Expand Up @@ -178,10 +178,12 @@ metadata1 <- metadata1 %>% dplyr::rename(
)
```

# QC metrics: raw data {.tabset}
# QC metrics: raw data

In this section, we review quality control (QC) metrics for the **raw feature matrices** generated by `Cellranger`. Only a low level filter excluding cells with <100 nUMIs (= number of unique molecular identifiers, or sequenced reads per cell) was applied when uploading the data into `R`.

:::{.panel-tabset}

## Cells per sample

```{r cells raw}
Expand Down Expand Up @@ -351,13 +353,16 @@ metadata0 %>%
theme(plot.title = element_text(hjust = 0.5, face = "bold"))
```

:::

# QC metrics: Filtered data {.tabset}
# QC metrics: Filtered data

Based on the above QC metrics, we filtered the dataset to isolate cells passing the following thresholds: >`r nCount_RNA_cutoff` UMIs, >`r nFeature_RNA_cutoff` genes, <`r mitoRatio_cutoff` mitochondrial gene ratio, and >`r Log10GenesPerUMI_cutoff` complexity.

In this section, we review QC metrics for our filtered dataset.

:::{.panel-tabset}

## Cells per sample

```{r cells filtered}
Expand Down Expand Up @@ -521,6 +526,7 @@ metadata1 %>%
theme(plot.title = element_text(hjust = 0.5, face = "bold"))
```

:::

# R session

Expand Down
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